# HG changeset patch
# User iuc
# Date 1504048321 14400
# Node ID 961a712f974319b84137e7c7cbee8776c6eff2fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
diff -r 000000000000 -r 961a712f9743 codeml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/codeml.xml Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,465 @@
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+ Detects positive selection (paml package)
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+ macros.xml
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+ paml
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+ &1 | tail -1 ]]>
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+ AAs
+ CodonFreq = $adv.CodonFreq * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+ clock = $adv.clock * 0:no clock, 1:clock; 2:local clock
+ aaDist = $adv.aaDist * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+ * 7:AAClasses
+ aaRatefile = $adv.aaRateFile * only used for aa seqs with model=empirical(_F)
+ * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+ model = $compat_model.brmodel
+ * models for codons:
+ * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+ * models for AAs or codon-translated AAs:
+ * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
+ * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
+ NSsites = $compat_model.NSsites * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+ * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+ * 13:3normal>0
+ icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below
+ Mgene = $adv.Mgene * 0:rates, 1:separate;
+ fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated
+ kappa = $adv.kappa * initial or fixed kappa
+ fix_omega = $adv.fix_omega * 1: omega or omega_1 fixed, 0: estimate
+ omega = $adv.omega * initial or fixed omega, for codons or codon-based AAs
+ fix_alpha = $adv.fix_alpha * 0: estimate gamma shape parameter; 1: fix it at alpha
+ alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate)
+ Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha
+ ncatG = $adv.ncatG * # of categories in dG of NSsites models
+ fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho
+ rho = $adv.rho * initial or fixed rho, 0:no correlation
+ getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+ Small_Diff = $adv.Small_Diff
+ cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
+ fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
+ method = $adv.method * 0: simultaneous; 1: one branch at a time
+
+ ]]>
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+ adv['seqtype']=="1"
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+ adv['seqtype']=="1"
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+ adv['seqtype']=="1"
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+ adv['verbose']=="1"
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+ If fix_kappa = 1 (fixed), the value of kappa is the given value
+ -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
+
+ - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
+ - 'fix_alpha' works in a similar way that fix_kappa.
+ -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
+ -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
+
+ - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
+ -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
+ -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
+ -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
+ -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
+
+----------
+
+**Output files**
+
+- codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run).
+- run_codeml : main result file name.
+- The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values;
+- lnf, rst and rst1: Supplemental results.
+- rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood).
+
+----------
+
+**How to edit manually the tree file : Branch or node labels**
+
+Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
+
+ - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
+
+ - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
+
+ - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
+
+In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
+ The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.
+
+The following trees are equivalent :
+ ((rabbit, rat) $1, human), goat_cow, marsupial);
+ (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
+
+$ is the symbol for clade labels.
+
+Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root.
+
+In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
+ $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade.
+ Equivalent tree with only '#' :
+ ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
+
+
+ ]]>
+
+
+ 10.1093/molbev/msm088
+
+
diff -r 000000000000 -r 961a712f9743 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Aug 29 19:12:01 2017 -0400
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\ No newline at end of file
diff -r 000000000000 -r 961a712f9743 test-data/1_2ngdn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_2ngdn Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 0.0628
+Ap 0.0536 0.0422
+Pg 0.1215 0.0396 0.1403
+Th 0.0137 0.0000 0.0932 0.0625
+Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/1_2ngds
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_2ngds Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.4398
+Ap 0.1327 1.2410
+Pg 0.5783 3.0000 0.3631
+Th 2.0454 0.0066 1.0019 4.0052
+Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/1_2ngt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_2ngt Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.1652
+Ap 0.2186 0.9823
+Pg 0.6879 2.1378 0.5820
+Th 1.4515 0.0048 0.9174 2.9292
+Ph 0.7412 1.2821 0.5897 0.5567 -nan
diff -r 000000000000 -r 961a712f9743 test-data/1_codeml.ctl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_codeml.ctl Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,45 @@
+
+ seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_1.dat * sequence data file name
+ outfile = run_codeml * main result file name
+ treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_2.dat * tree structure file name
+ noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
+ verbose = 0 * 1: detailed output, 0: concise output
+ runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
+ * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+ seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
+ CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+ clock = 0 * 0:no clock, 1:clock; 2:local clock
+ aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+ * 7:AAClasses
+ aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
+ * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+ model = 0
+ * models for codons:
+ * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+ * models for AAs or codon-translated AAs:
+ * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
+ * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
+ NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+ * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+ * 13:3normal>0
+ icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below
+ Mgene = 0 * 0:rates, 1:separate;
+ fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
+ kappa = 2.0 * initial or fixed kappa
+ fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
+ omega = 0.2 * initial or fixed omega, for codons or codon-based AAs
+ fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
+ alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate)
+ Malpha = 0 * 1: different alphas for genes, 0 : one alpha
+ ncatG = 3 * # of categories in dG of NSsites models
+ fix_rho = 1 * 0: estimate rho; 1: fix it at rho
+ rho = 0.0 * initial or fixed rho, 0:no correlation
+ getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+ Small_Diff = 5e-07
+ cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
+ fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
+ method = 0 * 0: simultaneous; 1: one branch at a time
+
+
\ No newline at end of file
diff -r 000000000000 -r 961a712f9743 test-data/1_run_codeml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_run_codeml Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,152 @@
+CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_1.dat
+Model: One dN/dS ratio for branches,
+Codon frequency model: F1x4
+ns = 6 ls = 13754
+
+Codon usage in sequences
+--------------------------------------------------------------------------------------------------------------------------------------
+Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40
+ TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34
+Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
+ TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27
+--------------------------------------------------------------------------------------------------------------------------------------
+Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25
+ CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39
+ CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17
+ CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11
+--------------------------------------------------------------------------------------------------------------------------------------
+Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39
+ ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40
+ ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30
+Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23
+--------------------------------------------------------------------------------------------------------------------------------------
+Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34
+ GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41
+ GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26
+ GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24
+--------------------------------------------------------------------------------------------------------------------------------------
+
+Codon position x base (3x4) table for each sequence.
+
+#1: Ac
+position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210
+position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767
+position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232
+Average T:0.27704 C:0.24321 A:0.24905 G:0.23070
+
+#2: Am
+position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269
+position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611
+position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689
+Average T:0.19140 C:0.26973 A:0.26031 G:0.27856
+
+#3: Ap
+position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243
+position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521
+position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042
+Average T:0.28066 C:0.24824 A:0.24175 G:0.22935
+
+#4: Pg
+position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604
+position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839
+position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761
+Average T:0.27943 C:0.23894 A:0.27762 G:0.20401
+
+#5: Th
+position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642
+position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623
+position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572
+Average T:0.20850 C:0.27659 A:0.24546 G:0.26946
+
+#6: Ph
+position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682
+position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737
+position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074
+Average T:0.26575 C:0.25975 A:0.24286 G:0.23164
+
+Sums of codon usage counts
+------------------------------------------------------------------------------
+Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547
+ TTC 765 | TCC 595 | TAC 364 | TGC 398
+Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0
+ TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445
+------------------------------------------------------------------------------
+Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259
+ CTC 418 | CCC 233 | CAC 400 | CGC 215
+ CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217
+ CTG 651 | CCG 181 | CAG 553 | CGG 153
+------------------------------------------------------------------------------
+Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378
+ ATC 623 | ACC 405 | AAC 516 | AGC 441
+ ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431
+Met M ATG 832 | ACG 230 | AAG 661 | AGG 374
+------------------------------------------------------------------------------
+Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397
+ GTC 531 | GCC 585 | GAC 513 | GGC 435
+ GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405
+ GTG 592 | GCG 159 | GAG 424 | GGG 202
+------------------------------------------------------------------------------
+
+(Ambiguity data are not used in the counts.)
+
+
+Codon position x base (3x4) table, overall
+
+position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819
+position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582
+position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601
+Average T:0.27338 C:0.24787 A:0.24874 G:0.23001
+
+
+Nei & Gojobori 1986. dN/dS (dN, dS)
+(Pairwise deletion)
+(Note: This matrix is not used in later ML. analysis.
+Use runmode = -2 for ML pairwise comparison.)
+
+Ac
+Am 0.0436 (0.0628 1.4398)
+Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
+Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
+Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052)
+Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000)
+NOTE: -1 means that NG86 is inapplicable.
+
+
+TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1
+lnL(ntime: 9 np: 11): -71862.094834 +0.000000
+ 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
+ 0.246863 0.000004 0.279150 0.179426 0.225632 0.000004 0.478467 0.076909 0.146872 3.015798 0.345817
+
+Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
+
+tree length = 1.63333
+
+(((4: 0.279150, 2: 0.179426): 0.000004, 5: 0.225632): 0.246863, (6: 0.478467, 3: 0.076909): 0.000004, 1: 0.146872);
+
+(((Pg: 0.279150, Am: 0.179426): 0.000004, Th: 0.225632): 0.246863, (Ph: 0.478467, Ap: 0.076909): 0.000004, Ac: 0.146872);
+
+Detailed output identifying parameters
+
+kappa (ts/tv) = 3.01580
+
+omega (dN/dS) = 0.34582
+
+dN & dS for each branch
+
+ branch t N S dN/dS dN dS N*dN S*dS
+
+ 7..8 0.247 29225.7 12036.3 0.3458 0.0530 0.1533 1549.7 1845.6
+ 8..9 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0
+ 9..4 0.279 29225.7 12036.3 0.3458 0.0600 0.1734 1752.4 2087.0
+ 9..2 0.179 29225.7 12036.3 0.3458 0.0385 0.1114 1126.4 1341.4
+ 8..5 0.226 29225.7 12036.3 0.3458 0.0485 0.1401 1416.5 1686.9
+ 7..10 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0
+ 10..6 0.478 29225.7 12036.3 0.3458 0.1028 0.2972 3003.7 3577.1
+ 10..3 0.077 29225.7 12036.3 0.3458 0.0165 0.0478 482.8 575.0
+ 7..1 0.147 29225.7 12036.3 0.3458 0.0315 0.0912 922.0 1098.1
+
+tree length for dN: 0.3508
+tree length for dS: 1.0145
+
+
+Time used: 1:09
diff -r 000000000000 -r 961a712f9743 test-data/2_2ngdn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_2ngdn Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 0.0628
+Ap 0.0536 0.0422
+Pg 0.1215 0.0396 0.1403
+Th 0.0137 0.0000 0.0932 0.0625
+Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/2_2ngds
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_2ngds Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.4398
+Ap 0.1327 1.2410
+Pg 0.5783 3.0000 0.3631
+Th 2.0454 0.0066 1.0019 4.0052
+Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/2_2ngt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_2ngt Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.1652
+Ap 0.2186 0.9823
+Pg 0.6879 2.1378 0.5820
+Th 1.4515 0.0048 0.9174 2.9292
+Ph 0.7412 1.2821 0.5897 0.5567 -nan
diff -r 000000000000 -r 961a712f9743 test-data/2_codeml.ctl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_codeml.ctl Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,45 @@
+
+ seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_12.dat * sequence data file name
+ outfile = run_codeml * main result file name
+ treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_13.dat * tree structure file name
+ noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
+ verbose = 0 * 1: detailed output, 0: concise output
+ runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
+ * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+ seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
+ CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+ clock = 0 * 0:no clock, 1:clock; 2:local clock
+ aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+ * 7:AAClasses
+ aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
+ * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+ model = 2
+ * models for codons:
+ * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+ * models for AAs or codon-translated AAs:
+ * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
+ * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
+ NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+ * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+ * 13:3normal>0
+ icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below
+ Mgene = 0 * 0:rates, 1:separate;
+ fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
+ kappa = 2.0 * initial or fixed kappa
+ fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
+ omega = 0.2 * initial or fixed omega, for codons or codon-based AAs
+ fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
+ alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate)
+ Malpha = 0 * 1: different alphas for genes, 0 : one alpha
+ ncatG = 3 * # of categories in dG of NSsites models
+ fix_rho = 1 * 0: estimate rho; 1: fix it at rho
+ rho = 0.0 * initial or fixed rho, 0:no correlation
+ getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+ Small_Diff = 5e-07
+ cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
+ fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
+ method = 0 * 0: simultaneous; 1: one branch at a time
+
+
\ No newline at end of file
diff -r 000000000000 -r 961a712f9743 test-data/2_run_codeml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_run_codeml Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,160 @@
+CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_12.dat
+Model: several dN/dS ratios for branches for branches,
+Codon frequency model: F1x4
+ns = 6 ls = 13754
+
+Codon usage in sequences
+--------------------------------------------------------------------------------------------------------------------------------------
+Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40
+ TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34
+Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
+ TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27
+--------------------------------------------------------------------------------------------------------------------------------------
+Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25
+ CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39
+ CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17
+ CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11
+--------------------------------------------------------------------------------------------------------------------------------------
+Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39
+ ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40
+ ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30
+Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23
+--------------------------------------------------------------------------------------------------------------------------------------
+Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34
+ GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41
+ GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26
+ GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24
+--------------------------------------------------------------------------------------------------------------------------------------
+
+Codon position x base (3x4) table for each sequence.
+
+#1: Ac
+position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210
+position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767
+position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232
+Average T:0.27704 C:0.24321 A:0.24905 G:0.23070
+
+#2: Am
+position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269
+position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611
+position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689
+Average T:0.19140 C:0.26973 A:0.26031 G:0.27856
+
+#3: Ap
+position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243
+position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521
+position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042
+Average T:0.28066 C:0.24824 A:0.24175 G:0.22935
+
+#4: Pg
+position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604
+position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839
+position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761
+Average T:0.27943 C:0.23894 A:0.27762 G:0.20401
+
+#5: Th
+position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642
+position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623
+position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572
+Average T:0.20850 C:0.27659 A:0.24546 G:0.26946
+
+#6: Ph
+position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682
+position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737
+position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074
+Average T:0.26575 C:0.25975 A:0.24286 G:0.23164
+
+Sums of codon usage counts
+------------------------------------------------------------------------------
+Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547
+ TTC 765 | TCC 595 | TAC 364 | TGC 398
+Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0
+ TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445
+------------------------------------------------------------------------------
+Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259
+ CTC 418 | CCC 233 | CAC 400 | CGC 215
+ CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217
+ CTG 651 | CCG 181 | CAG 553 | CGG 153
+------------------------------------------------------------------------------
+Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378
+ ATC 623 | ACC 405 | AAC 516 | AGC 441
+ ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431
+Met M ATG 832 | ACG 230 | AAG 661 | AGG 374
+------------------------------------------------------------------------------
+Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397
+ GTC 531 | GCC 585 | GAC 513 | GGC 435
+ GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405
+ GTG 592 | GCG 159 | GAG 424 | GGG 202
+------------------------------------------------------------------------------
+
+(Ambiguity data are not used in the counts.)
+
+
+Codon position x base (3x4) table, overall
+
+position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819
+position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582
+position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601
+Average T:0.27338 C:0.24787 A:0.24874 G:0.23001
+
+
+Nei & Gojobori 1986. dN/dS (dN, dS)
+(Pairwise deletion)
+(Note: This matrix is not used in later ML. analysis.
+Use runmode = -2 for ML pairwise comparison.)
+
+Ac
+Am 0.0436 (0.0628 1.4398)
+Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
+Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
+Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052)
+Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000)
+NOTE: -1 means that NG86 is inapplicable.
+
+
+TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1
+lnL(ntime: 9 np: 14): -71787.227810 +0.000000
+ 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
+ 0.289241 0.000004 0.219684 0.262034 0.350843 0.000004 0.491088 0.068009 0.152428 3.034323 0.539520 0.332686 0.087098 0.034121
+
+Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
+
+tree length = 1.83334
+
+(((4: 0.219684, 2: 0.262034): 0.000004, 5: 0.350843): 0.289241, (6: 0.491088, 3: 0.068009): 0.000004, 1: 0.152428);
+
+(((Pg: 0.219684, Am: 0.262034): 0.000004, Th: 0.350843): 0.289241, (Ph: 0.491088, Ap: 0.068009): 0.000004, Ac: 0.152428);
+
+Detailed output identifying parameters
+
+kappa (ts/tv) = 3.03432
+
+w (dN/dS) for branches: 0.53952 0.33269 0.08710 0.03412
+
+dN & dS for each branch
+
+ branch t N S dN/dS dN dS N*dN S*dS
+
+ 7..8 0.289 29216.6 12045.4 0.5395 0.0772 0.1431 2255.0 1723.2
+ 8..9 0.000 29216.6 12045.4 0.0871 0.0000 0.0000 0.0 0.0
+ 9..4 0.220 29216.6 12045.4 0.0871 0.0180 0.2071 527.0 2494.5
+ 9..2 0.262 29216.6 12045.4 0.0871 0.0215 0.2470 628.6 2975.4
+ 8..5 0.351 29216.6 12045.4 0.0341 0.0126 0.3700 368.8 4456.6
+ 7..10 0.000 29216.6 12045.4 0.3327 0.0000 0.0000 0.0 0.0
+ 10..6 0.491 29216.6 12045.4 0.3327 0.1032 0.3103 3016.4 3738.0
+ 10..3 0.068 29216.6 12045.4 0.3327 0.0143 0.0430 417.7 517.7
+ 7..1 0.152 29216.6 12045.4 0.5395 0.0407 0.0754 1188.4 908.1
+
+tree length for dN: 0.2876
+tree length for dS: 1.3959
+
+dS tree:
+(((Pg: 0.207095, Am: 0.247017): 0.000004, Th: 0.369987): 0.143059, (Ph: 0.310329, Ap: 0.042976): 0.000003, Ac: 0.075391);
+dN tree:
+(((Pg: 0.018038, Am: 0.021515): 0.000000, Th: 0.012624): 0.077183, (Ph: 0.103242, Ap: 0.014298): 0.000001, Ac: 0.040675);
+
+w ratios as labels for TreeView:
+(((Pg #0.0870978 , Am #0.0870978 ) #0.0870978 , Th #0.0341211 ) #0.53952 , (Ph #0.332686 , Ap #0.332686 ) #0.332686 , Ac #0.53952 );
+
+
+Time used: 2:11
diff -r 000000000000 -r 961a712f9743 test-data/3_2ngdn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_2ngdn Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 0.0628
+Ap 0.0536 0.0422
+Pg 0.1215 0.0396 0.1403
+Th 0.0137 0.0000 0.0932 0.0625
+Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/3_2ngds
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_2ngds Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.4398
+Ap 0.1327 1.2410
+Pg 0.5783 3.0000 0.3631
+Th 2.0454 0.0066 1.0019 4.0052
+Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
diff -r 000000000000 -r 961a712f9743 test-data/3_2ngt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_2ngt Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,7 @@
+ 6
+Ac
+Am 1.1652
+Ap 0.2186 0.9823
+Pg 0.6879 2.1378 0.5820
+Th 1.4515 0.0048 0.9174 2.9292
+Ph 0.7412 1.2821 0.5897 0.5567 -nan
diff -r 000000000000 -r 961a712f9743 test-data/3_codeml.ctl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_codeml.ctl Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,45 @@
+
+ seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_23.dat * sequence data file name
+ outfile = run_codeml * main result file name
+ treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_24.dat * tree structure file name
+ noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
+ verbose = 0 * 1: detailed output, 0: concise output
+ runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
+ * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+ seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
+ CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+ clock = 0 * 0:no clock, 1:clock; 2:local clock
+ aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+ * 7:AAClasses
+ aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
+ * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+ model = 3
+ * models for codons:
+ * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+ * models for AAs or codon-translated AAs:
+ * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
+ * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
+ NSsites = 2 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+ * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+ * 13:3normal>0
+ icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below
+ Mgene = 0 * 0:rates, 1:separate;
+ fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
+ kappa = 2.0 * initial or fixed kappa
+ fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
+ omega = 0.2 * initial or fixed omega, for codons or codon-based AAs
+ fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
+ alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate)
+ Malpha = 0 * 1: different alphas for genes, 0 : one alpha
+ ncatG = 3 * # of categories in dG of NSsites models
+ fix_rho = 1 * 0: estimate rho; 1: fix it at rho
+ rho = 0.0 * initial or fixed rho, 0:no correlation
+ getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+ Small_Diff = 5e-07
+ cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
+ fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
+ method = 0 * 0: simultaneous; 1: one branch at a time
+
+
\ No newline at end of file
diff -r 000000000000 -r 961a712f9743 test-data/3_run_codeml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_run_codeml Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,172 @@
+CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_23.dat
+Model: NSbranch3 for branches,
+Codon frequency model: F1x4
+Site-class models: PositiveSelection
+ns = 6 ls = 13754
+
+Codon usage in sequences
+--------------------------------------------------------------------------------------------------------------------------------------
+Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40
+ TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34
+Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
+ TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27
+--------------------------------------------------------------------------------------------------------------------------------------
+Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25
+ CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39
+ CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17
+ CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11
+--------------------------------------------------------------------------------------------------------------------------------------
+Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39
+ ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40
+ ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30
+Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23
+--------------------------------------------------------------------------------------------------------------------------------------
+Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34
+ GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41
+ GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26
+ GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24
+--------------------------------------------------------------------------------------------------------------------------------------
+
+Codon position x base (3x4) table for each sequence.
+
+#1: Ac
+position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210
+position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767
+position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232
+Average T:0.27704 C:0.24321 A:0.24905 G:0.23070
+
+#2: Am
+position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269
+position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611
+position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689
+Average T:0.19140 C:0.26973 A:0.26031 G:0.27856
+
+#3: Ap
+position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243
+position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521
+position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042
+Average T:0.28066 C:0.24824 A:0.24175 G:0.22935
+
+#4: Pg
+position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604
+position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839
+position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761
+Average T:0.27943 C:0.23894 A:0.27762 G:0.20401
+
+#5: Th
+position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642
+position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623
+position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572
+Average T:0.20850 C:0.27659 A:0.24546 G:0.26946
+
+#6: Ph
+position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682
+position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737
+position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074
+Average T:0.26575 C:0.25975 A:0.24286 G:0.23164
+
+Sums of codon usage counts
+------------------------------------------------------------------------------
+Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547
+ TTC 765 | TCC 595 | TAC 364 | TGC 398
+Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0
+ TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445
+------------------------------------------------------------------------------
+Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259
+ CTC 418 | CCC 233 | CAC 400 | CGC 215
+ CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217
+ CTG 651 | CCG 181 | CAG 553 | CGG 153
+------------------------------------------------------------------------------
+Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378
+ ATC 623 | ACC 405 | AAC 516 | AGC 441
+ ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431
+Met M ATG 832 | ACG 230 | AAG 661 | AGG 374
+------------------------------------------------------------------------------
+Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397
+ GTC 531 | GCC 585 | GAC 513 | GGC 435
+ GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405
+ GTG 592 | GCG 159 | GAG 424 | GGG 202
+------------------------------------------------------------------------------
+
+(Ambiguity data are not used in the counts.)
+
+
+Codon position x base (3x4) table, overall
+
+position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819
+position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582
+position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601
+Average T:0.27338 C:0.24787 A:0.24874 G:0.23001
+
+
+Nei & Gojobori 1986. dN/dS (dN, dS)
+(Pairwise deletion)
+(Note: This matrix is not used in later ML. analysis.
+Use runmode = -2 for ML pairwise comparison.)
+
+Ac
+Am 0.0436 (0.0628 1.4398)
+Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
+Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
+Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052)
+Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000)
+NOTE: -1 means that NG86 is inapplicable.
+
+
+TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1
+lnL(ntime: 9 np: 15): -71845.285288 +0.000000
+ 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1
+ 0.253789 0.000004 0.294642 0.199868 0.242499 0.000004 0.471201 0.102634 0.122472 3.060446 0.693669 0.106076 0.279090 0.015724 0.820701
+
+Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
+
+tree length = 1.68711
+
+(((4: 0.294642, 2: 0.199868): 0.000004, 5: 0.242499): 0.253789, (6: 0.471201, 3: 0.102634): 0.000004, 1: 0.122472);
+
+(((Pg: 0.294642, Am: 0.199868): 0.000004, Th: 0.242499): 0.253789, (Ph: 0.471201, Ap: 0.102634): 0.000004, Ac: 0.122472);
+
+Detailed output identifying parameters
+
+kappa (ts/tv) = 3.06045
+
+
+MLEs of dN/dS (w) for site classes (K=3)
+
+site class 0 1 2
+proportion 0.69367 0.10608 0.20025
+branch type 0: 0.27909 1.00000 0.01572
+branch type 1: 0.27909 1.00000 0.82070
+
+
+Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
+
+The grid (see ternary graph for p0-p1)
+
+w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
+w2: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
+w3: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850
+
+
+Posterior on the grid
+
+w0: 0.000 0.016 0.738 0.171 0.066 0.006 0.002 0.000 0.000 0.000
+w2: 0.988 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+w3: 0.000 0.828 0.064 0.033 0.057 0.014 0.001 0.001 0.000 0.001
+
+Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)
+
+ 0.000
+ 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.001 0.001 0.010 0.010 0.072 0.038 0.202 0.053 0.170 0.020 0.034 0.002 0.046 0.000 0.006 0.000 0.000
+ 0.000 0.000 0.000 0.003 0.004 0.039 0.014 0.031 0.010 0.101 0.007 0.020 0.001 0.026 0.001 0.072 0.003 0.001 0.000
+
+sum of density on p0-p1 = 1.000000
+
+Time used: 4:22
diff -r 000000000000 -r 961a712f9743 test-data/RAxML_bestTree
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAxML_bestTree Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,1 @@
+(((Pg:0.09616539105673740928,Am:0.18952716489066595562):0.03831049025178590028,Th:0.15207937554419623249):0.09631839546127254903,(Ph:0.14632947629352840990,Ap:0.01138142236754203541):0.01631824366568397633,Ac:0.01822503877829063923):0.0;
diff -r 000000000000 -r 961a712f9743 test-data/concat.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concat.fasta Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,12 @@
+>Ac
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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aaaatggcgccaaaaaggaataatgttattccgaaccagcacttccgcaaggactggcagcgatgggtgaagggatggttcaaccagcccgcccgcaagaagaggaggagggacacccgccagaagaaggctcgcaccattgccccacggccggtcaaggccctcaggcccgcagtgcgctgtatgaccttcaaatacaactccaagatccgactgggacgaggcttctcgctggatgaactcaaacaagccggtctgaacaaggacttcgccaggaccatcggtatctcggtggaccaccgacgccggaaccgatccgtcgagtcgctgcagatgaacgtccagaggctgaaggagtacaagagcaagctgatcctgttccccagaaagaccagcaagcccaagaagggtgatgcaactgaggaggagatcaagatggcgacccagaccccgggcatcgtgatgccgctgccgaagcccgtcgctcgccgagagaaggcccgcgccgtcacggacgaggagaagggccacagcgttttcgtggcgctgcgacagggacgcgccgacactcgattggtcggagtgcgcgcgaagaaggccaaggaggcagccgaggccaacagcatggatcaggttgtgcagtttgtcgagccggcaaagcagtttgcgaaggactccatccgattggtgaaaagatgcaccaagccagatcgcaaagaatttcagaagattgccatggcgactgcgataggatttgctatcatgggtttcatcggattctttgtcaaattaatccacattcccatcaacaacatcatcgtaggttca------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgttttgggattctgccatgcccactcaaaccgcaaagctgcaatctggtttggaaatccatggactatcaataccatgtcccatgggcctctgccacttgtttttttggcgccaccggcttgagtgcccctgttgtgttgtttgactcgtctgttgggatcaactgtgaaacctatgtacgtctgacctttatatttaggatttatacaata---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atcatgtctctgatcgtgccagagaagtttcagcacattctgcgtgttctcaacacgaacgaggaagaggtagagaaggtgatcacgatcatgtcgaaccctcgccagtacaagatcccggactggttcctgaacagacagaaggacgtcaaggacgggaagtacggccagattctgtctaacatcctcgacagcaagatccgagaggacctcgaacgactcaagaagatccgggctcaccgcgggctccgtcactactggggtctgcgcgtgcgaggccagcacaccaagacgaccgggcgacgtggacgaactgttggtgtctccaagaagaag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggggacgcctcgtcacggtcagccttcaccttcataccgccagtcacacgcacgatcgtctctttgccagacagatccgtgatgtggacgaatgtgtcattgaagctggcgaatatgtgtgctacaccaaaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Ap
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---------------------------------------------------------------------tctgatccatccataatggctgcatccatctggacttctcctttggcatttagggctgatccagtacctgcatcaaacacagagttgttctccatatccatgacagccaattccacaacatctagagcagatccaccatttaataagagctttaaccctttaagtgcagcctttttaaccccttgtctgttttgcatggccatgctgtctgggatggcccaagctccacca---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pg
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgtgagctctccaaaatcttcatatatgcagcttcagtttctgcgatggttttgtcaaattcattccttgatgccattttcttgctcaaactttcattaattttggcaagtttttcagtcagaatccggatgtcattctggacttttctcttctcctcctcttcatctaggatttgtttctggagctcatccctctttgtacaaagatcttctatgcattttaccagttcattatta---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tctagtgacacctggttgtatgattctattttaatatctgcagatccactgttgattcttactggtccctgttctgcctggatagtaacaccttctggagctgacaaatctaagctacgtgttggtgattctaacctgagactaccagtctttgatctgacgacaggagtttggactgaacccggagtagagcaaaaggagatacgtgttggtcagccaaactgtaaactgtccaagtatcgattttatatgggtgatgaacgtgtcttggcaccaatggccatgttctacccaaacatgctgggtctgataggaaccaatgtttgtaaaaacatggacagatactgtagtgatccagctgatcttggagcttggatgccatttgcagcagacctcgatgagtccacctgtctccgtggtaaccgttctaactgttgcctagttgactgcagttgcatttctaactgctgcaactgtgatgacacactcaaggaattgatgaacaaacttcagattgaacatgatgtagatgctagtctgcgtggtgtgatgagagatttacatgatgcaagaatgaaacagctgagggaactccagaaggatattgctgctgataattggcgatacactccaatagagaaattaatcggtttgcaacaggtgaggcctctcctccaatttgtcatattccaagtggaattcctttgccactttgcgccaattctgtacatcaaaataatagtatgtgcctcgttcatatgtatttgttttcacaacaggctccatgcccggtgctcgagtgatccacactcgctcctctttgtgataccgccaatctctttgatacagttcagcagctgctgcgtcaattgcctcaaatccctgaagttgatgaggacatttttccctgtaaatttctggtccatcttcttgtttcttgtctatttcatggtttactctataccacgcttctgccatatatttgacattctcttcatgctgttgtacgcaagcactatcttgatgtgtcatcatactattagacattccattcagaaagaggagatgtcccggctgacgaagatcccaacagaggatttcaggatcctttcttcctccgctgtagagcctcgtaccgtcacgcgagaacatgatatgggtgacgccgccctgctgaccttgaaacatgcacagcatcttgcccgacttctccgtgtacaaggcaacggacgttttctcttcttggctgtagctatggcagcagcagcagcaacaccaatgggaccggctgatacaagctgcgctgtaacctcatcattaacagttgcattgaggatgtctgagtcgtcgaaatctgcatcctcttcggatgttgcatcactgatggtatcactgatcatcgtggcacagttgcagactgctgtattctttatggaaagccgcttcaacttcaatttcaaacgcttcataatgaacctgttctctatctgctcatgcgtcttgaactcaaaaaatatacgagagaggcactccaacagttgctgcagatcaacaccatctgtgtccatgttgaagccaatgggaaaagtaacagctgcaacacaaaacatcaccattgcagcaaatccaagccatcgagcatatttcctcacctcactttcccagtacgaggcgataagcagagcaatggtgactgtaacacaaagtattcctgctaagacacacagaaatgtcaacccccattctggatggatttcagctggatcatacatgccaatatatcccgatggcaccgtcaggaatctgtatattatccaaactgtcattggtatattga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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gagccagcaaagcagtttgcaaaagattctatacgactggttaaaagatgcaccaaaccagatagaagagaattccagaagatagccatggcaactgctattggttttgctattatggggtttatcggatttttcgttaagctgatccatataccaatcaacaacatcattgtgggttcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ccagctatgaaagatgtgtttgttgtcttccactgtgcaactccttcaccattgagtaataacaaagaactgtttcacaaggttaattgtcagggtacaaaaaacatcatagaagcctgtaaagaggctggtgtgaagaggctagttttaacgagcagtgctagtgttgtgtatgaagggaaggatgtagaaaatggtacagaacttatatgcctg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tccctctctatttcttcaacagtttttagtgtaatgccttcagaccgaagtgattccgctattttattgaatatagattcctcctccacaccagacttagccatatcactgtacatagttataaatctttcacttaaaggtacagattttgaatctttcatgtcaataatatctggactgccaaacatcttgacatcggaacaactattaatctcaccatcctcaaaaaggtcaaactttgtggcaccatctattgcccaggaacagaattttccaagaccaactgtgatgacaattgcactggacagtgtcataaacattattatcatgtttatgaacataaacagagggttgatgctcataaca------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtcagctttcagacagcggaatgccgactacattgctacgaatgtgccacgtcgaccttgccatctatgtcccgacaagactgcctcgacggcaaagcggagttcgtacagtgcgggaccactgataaatactgcgtgatgttacgatacaccgaacacgaatctcaaggacacgacgctaacgacataggaatgttaatgtcagctggaacctcagcacgagctatttctgtgaacgttttcgcatccaacacgagcagaaaagactgcaaatcatcctttgttctaatcataggtgataagataataccatcatcctcttctcaatcagctgatctgacatattcgcatcatcttcctcagcttcctcagcatcttcatcataatcctcaccttgctcagccctgtaacttgctagagcatcctggtactcctggttgtctggatcgtgaccagcacgatgccgcaataggttgcccttgtgagcaaatgccttgtcacagtctggacactcatggatcttatcctttggagctggtggcacatagtctggattgtggtagaggttcttgtgcctctggcacccacgtgatgaagagtagaaagttaacgaggacacagatggcggcgaacatgccaaagcaccggatggctgtgacgtcgttgacgaagttcgccaatagggccgtcgacgtcgtgaagctcgtcacaaacaccgacgtgccgcccttgcggagcgtgtgcgagataagctcctcgtgtccacttcagacatcttgtatcctgatgtgtaccgagacatctgacagtacagtaacgagctccacactgtacacaggtatagttagatggaaaaccacaaacactacagaagtgtctctccggaaagtgagatggtggcacacatgccgtctggtagccaggcaaatcaccagtcatcatttgctcttcttcaaggagtgctgcaaagttctttctgaatcgttccttgaaaatatcacttcttcgttttttcttctttctgccaacttgttaaatgtctttccattgtatacaccaacaatgctgccaatcatttcaggaacaataatcatatcacgtaaatgtgtcttgatacactctggcttttccattggaggtgcctccttcttggctttgcgaaggcgtttaatgagagccattggtttacgcttcaaaccacgggagaaacgtctgcgagcccgacaagtggacttgagctttcttttgttttctaatgtagtgatgacattctggtacttccagcccacttcatgtgacaggcggccaagaacacatgacttgcgtctagctttaagtcgaaggaccttcaaagccgagggaaccaccatacgtttctgcttgtcaaatggtggagggatgccctcaaagaccttgagacggtccagagcttgcttaccacgtgtcagcttatgtggcaacataccacgcacagttctccaaaatattttacttggggcacggaagtggtatgggccacggcttggattggtgttcattcgtttccttaggaaagcaaggtacttcagtttgttcctgatggagtacaacccacactccatcaccagctttgttaacttgttctacataatctgctctagatatttccattacactaccaaactgagcagatttatatgcttgctgcatctcggccattcttttccgtcgatattcttcaaatattctttcttcctcttcatcaatttcatcttctttttcattgccagcctgagtaaatctgaagatgttgtcaataaagagcagcacgtcctgtccttctacatcacggaaatattcggcaacagtcaaaccggtcagagctacgcgagcacgggcacctggaggctcattcatttgaccatacaccaacgacaccttagaagacttgtccttcagactgatcacaccaccctcaatcatctcatgatacaagtcattgccctcacgggtacgttctccaacaccagcaaacaccgagtagccaccatgtgccttggccacattgttaatcagttccatgatcaacacagtcttaccgacaccagcaccaccaaacagaccaatttttccacccttagcataaggggccaacatgtcgataactttaattccagtctccaggatttcttgttcaagactcatctcaacaaatgctggcgcctcagcatggattttcttaggtacagtaccttcacggaatccattcctaaatcttctgaagaccttcttcatatgcctcatacgtcctacaccttgggtcctcctcctcttcgccttctcactccagttgtattttctcattcttttagcaggatatccgcaactggcacaagtcttcttctgtatgtggtaacatctgccaccacaacgacgacacagtgtgtgtgtcttgttgtggcgttttccaa----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgtctggagatgaaacaagacagcggcccgatttctgtaaagatgccaaccttgttaacctgtgtcacgacagcctccagtacttctcctttaaacggtcgaaacacgatggctttgtacttgatcggataaacaacaaaacctcggctcggctgaatgaggccagctccaatgtcatcaataattgtcacggcaacgacgaaaccatattttccagtacaggttccttccacttcagtaaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acaacttctcctttaaagttcatcccttctacaaccatttcagctgccttttttatagacacttcatcttcttctccaactgaaagaatgattggatcaatctctggatattctctaagtacccagataaagagtctcgcaagatccagagaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Th
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gttttacggggtagcttcttggggtgccaacgcgaggtcacacccttgaatccttttcctttggtcacaccaatgacatcaatgaattcatcttgtgcaaacacctcttccagtggtacggtcttttcaaagtgttcccgtgcccagtctaccttttgggcaatggtacctccattgagttggatctccatgatgtgggctttcttttggcgtttcttaagaagcttcatctgggtgtgtgcaatcactctgatcacagtgcagtacttcttgatcttgttaaggtccttttcgatctcctttttaccaaggtcatcctgccacttcttggtggctttggtgaatgccttcttcttggacttgtacatgccgaaagtccgccgcagccggaagcccccgcccgacggctgggagctgatcgagccgacactggacgaactcgaccagaagatgcgcgaggccgagacggagtcgcacgagggcaagcgcaaggtcgagggcctgtggccgatcttccgcatccaccaccagaagtcgcgctacctcttcgaactcttctacaagcgcaaggccatcagccgcgagctctacgagttctgtctgaaggagaacatcgccgacaagaacctgatcgccaagtggaagaaacctggctacgagaacctgtgctgcctgcgctgcatccagacgagggacacaaatttcggcgcgaactgtgtctgtcgcgtgcccaagcccaagctggaggaggggaagatcgtcgagtgcgtgaactgtggctgtaggggttgtgcggacatgtccgaggacatgcagcaagatgccgtggactgcgccatgcaagcgctcgaaaagtacaacatcgagaaagacatcgcagccttcatcaagaaggaattcgacaagaagtacaacccaacgtggcactgcatcgtcggccgaaattttggcagctacgtcacgcacgagacaaaacatttcatctatttttacctcggccaagttgctatcctactcttcaagtcggaagtaattcaagttcatcgagaagtcatagtccttataaaggagttcgtaaaccctatcatccgaaaacatccaagcccttattcctcatactctgctagctcatcatctcatcataaatctgcaaaaagaggtaagcatgatcgtcatgat---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aaaatggcgccaaaaaggaataatgttattccgaaccagcacttccgcaaggactggcagcgatgggtgaagggatggttcaaccagcccgcccgcaagaagaggaggagggacacccgccagaagaaggctcgcaccattgctccacggccggtcaaggccctcaggcccgcagtgcgctgtatgaccttcaaatacaactccaagatccgactgggacgaggcttctcgctggatgaactcaaacaagccggtctgaacaaggacttcgccaggaccatcggtatctcggtggaccaccgacgccggaaccgatccgtcgagtcgctgcagatgaacgtccagaggctgaaggagtacaagagcaagctgatcctgttccccagaaagaccagcaagcccaagaagggtgatgcaactgaggaggagatcaagatggcgacccagaccccgggcatcgtgatgccgctgccgaagcccgtcgctcgccgagagaaggcccgcgccgtcacggacgaggagaagggccacagcgttttcgtggcgctgcgacagggacgcgccgacactcgattggtcggagtgcgcgcgaagaaggccaaggaggcagccgaggccaacagc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gcccgtaagatgaaggaccatcgtcgagaccagaaatggcacgacaaagattacaagaaaagccacttgggtactcgctggaaggccaacgccttcggaggtgcatcccatgccaagggaatcgtgctcgagaaagtaggtgttgaggccaagcagcccaactctgccatccgcaagtgtgtgcgagttcagctgatcaagaacggcaaaaagatcacggccttcgtaccgcgggacggttgtctcaactacattgaggagaacgatgaggtgctgatcgctggattcggacgaaagggccacgctgtcggagatattcccggcgttcgcttcaag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------accatacgcttctgcttgtcatatggaggggggatgccttcaaacactttcattctctccaaagctgccttgccacggggtaacttatgtggcaacattcctctgactgttctccagaaaatcttgctgggagcacggaagtggaatggaccacggcttggtttggtgttcatacgctttctaaggaaatccaagtacttgagt------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cctgcgggagcaccggctgttcacgtccaaccccaagctggactgttgtccgacggtgacggaactcgcccaccgaggcgtgggcatcaacccacagggcctgctcctcgagctgttccacacgcccaacttcacgcagactttctacgagaccgtgtgccacccgcacatcaaggaccggccgtgtcagttcatcgacagggagtacctgcagtactcgcgctgtacgcagcagtactcctacgtgtacgcgctcgggcggacctacggcacacatgctttgagtttcaaaatattagccgaatgttcgacatcaaaagcacgaatcagccagataactttgccacatggcttggtagatgccccagttttcatgccagttggaacacaagggacattgaaaggcttgattccagaacaactggagaatttgaactgtcaaataattcttggaaatacgtatcatttgggaaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacagagaagccatgcggcttgggccggtagtcgcagtggaagatctcgatgatctccccccgccgcttgccgccctcccacacgttaccgagcgtctccatgtagtccttggagacgtccgggtagttgtccagcagcaccaggttgttggtgcgcaccatccgccgcaggtggaagtagtccgacagactctccctgaacgtgtgaccgccgtcgatcacgacgatgtcacagcggaaatccttgttcgcttcccggaacctggg
+>Ph
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgggtgacgataataagagtaatgaacacattaatctcaaagtgacgggacaagatggaagtgttgtccattttaaaatcaagaaaaacactcctctgcggaagctgatgaatgcctattgtgacagaactggtgttaaaagtggtgccatgcggttccgttttgatggccagccaatcaatgagacggacactcctacacagttggatatggaagatggcgatgtgatcgacgtattccagcagcagactgggggc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttctctgataccgctttccttcagagtcactcggaatcctttgataatattgccatatttgtcagggtcaacctgcatgcggcacttgaccagatccaggggtacgacggctgtgtgagtgatcccacaactcaggatgccaccgaaaccacagagggcaaagaatttcgcactgccatattcacagctctccccctctgctattgcagcagctgcaatactccgcgttggattaatctgcagcccatcatcacattgagcctgaaaaggact------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgccgtgtagttggggtttcccatgccgctgtttccataaccaccccccatgctgttgctgccgaagttgttgctatttccactgccgtaaccacctccgtagccactgccacttccaaagctgtcgttcatccccatgcccgatcccattccactgcccattccgcctcccattcggtttacccatgaagtctttgtcttcaattatcctcaggccagccttctccgacatgccaagcttcttcactaacgcctccgcaatgccgttggccttctcgaaatctgatcccgcccctgtcgtgactttgtcactaccaaatattaattcctctgcaacacgtccgccgagagcaacgtccatttcagccaaaagctgtaccttcgttagattatactggtccttttctgggataaacgccgtatacgaaaacaattctcagagttattacggacttggcgacccaatgaaagaggcaacgatgtactgccagcaggggaagcacgaccgcgaggtgcgccagcagctcgaggagaagttccccgggcacacgctggaggtcggctacgaggacttcatcaacaacccgatagcgtacaccgagttcttcttccgcttcgtcgacttcccgatcgactccgacgtcagcgactacataaccgcctacgccccgctgctccagaaggaggtcaacgactggttcgccgacgccccgtacaacgtcgcccgggacatccgcgacaagtgcaacgtgctctggtacgggaaggcctacggattcatgattgactggccaaccagtttagcattacgcaccatgtgtaacacctcttcatattttctgttgacaagagccaatttgaacttaaattccgtggcatcgatgccaagtactcgaggacgacattccctgtccagacagtacacctggttacctttgatgcgagtgatgcgtacattagctgacttgttgttaagacgccacagaatggtaccacagatctgtggcaggtatggcttgactcgcttaccaagagcatttaccactgtaccaaatccattcagcatcaccacatcctctgtcgtttgttcctggaaggcatataatatcccatcaatgagctgttcctcaagacgtgagtcaatgtcagctgagcccagattagccatgactttctctatggtctccatgaccatcttacgatattgttcagattcatctttcagatcatctaccacacgactgatgatttcagctgctccaactttattagcaatctccactgtggtgtcaacgagctgtctgagaagtatctacaggacagaggtgaccagatacttgttatattacacgccaaagtggcgcagaagtcttatggaaatgagaaaaggtttttctgcccaccgccgtgtatttacctctttggcaatggatggaagagaaaaagggagcagctggagagggatggctgcagtgagcaggacacacaggtctgtgccttcatgggcatccctgtacatatctgccagcttctgtgcttgcttcagctgccacttcagcgtctgtatttcttcatcctgtcgtattcttcctgctcctgtagatgccgacacattaaggacattttcattggttgaattcatgtgctgtttgcacatgtccagttctcgcagtagacgatctttctcactcatccatttcttttcatgggcacggtgttcatatagtcaacattacagagtatgttacccactctggtatcctgataggctggcggtaactgaaccgatgtactctggtcaaagtttgcttccagtgcaatgctcggaagttggtttaaaacataaatcccaacagtcaattcacgtaaaaagtgtcaaattcggatgcgatgtctatttctacaaactcctgcctatctccgcctttccttccaatacctgcatcatcatccatgtcatcttggcgagcaaaacatgcaccaaaactccaggtaaatgcaaacacatacagcttaccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------actgcggagaagatggtgagtactgtggtgaggaaggactgtactctggcgaggatggactatacttggggctggttggtgtgtatgtgggtgatgtgggcgagtactttggtgatgctggggagtatgaggggctggtcggagaatactgaggtgatgatggggtgtactgtggcgagc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------agcagcgtgaggttctgtttttcaagctgcttcaccttcttctgtagttgcatgttgttcaaatcacaagctttcactcgccgctccagtccatcaatgtattcctgcttgcgcttgcgactttcttttgctgacaccttatttctgatctttcgtcggacagacttcagcgcgcgttcttcctcctttgtcagtggcaggttc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttagttacctcggcttttactgtctgtggcgtcgattctacaaacttctttgcctgtacaagattcatgccagccataacattctttatctgtttaataagagctactttcttggcttcatcaaaaccagcaagtttaacggtaaatgccaccttttctggcttcttctctgatggcgtttcctcgtcttcctttggagcaatagccggcatggctcccatggccatcataggagtgtctgtaatgttcagtgttttttttaataac------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cgctctccctctttggcttttcctgcttttcctggtttagattttgcaaagagagctgggtccaattcatcaagctttttgcccttggttgaaaatagtctctgtgccctttcttccagggtacctccacatttcaggccaagagcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggaaccctgatattaatccactgatatatggaggccatgctttcctttcaaacatcggtgcatccggaagcttcatctggatttcacctgaccatgggaaaaggatttcaaatgcacagaccagtataccaaacatggccacaagtggtaaggcaagcacaaaatatggtgaacctatccatggattgctggactctttaatggatggtgccagtagtgaatcaaatacaggacaaagtatgcca---------atgacgcgcggcaaccagcgtgagttggctcgcctcaagaacttaaagaaacaacaacaagtggcaaagggaaagaaagcttcggaaaaaggggctaatgctggccagtccctacaggaaaggcgccatagggatgcagaacgaatgagagagaagcagcgtaaggcagaggagatgagacagaaacagtcg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctgtatggctgtgttggtgcaggctcatccttaggttcaactatgctgatgttgtcagggagtggacgctttgggcctatcttaccagagggatcccatggcagcataattttcactttgattcccagcacaccttgccttagcagcacatgtctaacagcagtgtccacatattcattgcacggctcaccactg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacgtacagcttggccgccacgcacacgtgagctcccatggcgaacgccagggcggcgccgagaccctgcagcatccggaagttctggaacgccacgtcgtggtcgtctggacagctgaggttaaccaaaaagttacactgggtctgccagatggcgtcgcagaggccccacagcgcggaaacgacgaagaacaccggaaacagcgtcttgtcgggaatccagaccaacaggaagaccatgatgccgatgtgcaggatactgcctactccgattatcgcctctcggggaaggttccgcgccacgatcccgatcaggatcgagaagag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgataccggaatattaatgtcggaaggaaccaaagcacgagcaatttctgtgaagctttttgcatccaataccagcagaaatgactgcagatcatcctttaatctgattacaggtgaaagtataacaccatcatcttcttctcaatcagctgattggacatatttggatcttcttcctcctcttcctcagcttcctcatcataatcctcacctcgttccgccctgtagtttgccaatgcctcctggtattcctgattatctggatcatgcccagctcggtgacgtagaaggttgcctttgtgagcaaatgccttatcacagtctggacactcatggatcttgtcctttggcgccggtggcacataatctggat------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gatggagttggtgatcgtgacatcggtatttcgacgtgtggcggtggtgatggtgatggcgagaaggtaaagtctggcacgatctccatgggagagttctgtttgatgactggcattacatcaagtgacatatctctcctcagtgatgcatctcgagaaggtcccaactcttccttcaactcatcaaagtctggctggttaagctcttcccaagccactgcttgctctttcagatctgtcacagcttctatgttatacatacattttctgatgacatcttctcggcctatcttcttcagtgctctctctaattcatttccagttgctctactcctgttcttcaacattgcctccttcatgatcagcgtgtatcatgaggtaaagcctcatcaactcgacgaacttcggatcctcgtatcccagcatcgagacgaaatttgctgcccagtccttttctggatcgatggcaccgacactggttccatccctgtacagatttctgtagatgatggcggctatcgtggggagttcagcgtgtatgggacggctattaaaccagcgattgttcagatcagccacagccttctccgcatcttcctcataacggaacttcacatagacatttccaacaagatgatcaccaagattgtcacagacgttcatctcctcaatctcaccatacttgtcctcgagttcttgatacatatggtggatggggtgcccatggtggtggcgctttctctggcaaagacttctccaaagttgatcgttctgctgcctatgctgctcgttgggtggctaagtctctggtcaaaggtggtctctgtcgacgtgtcttggtgcagctctcctatgccattggtg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgttgcagctgggatttgggcatgtccagtctcctgatcgacctgatccactgtcacgtccaccaggccatatctttcttgtagctgtctcaactttcagaactttacccatgaattctttattgttaaaccagctgatggctgattctgctgcctgc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aagaagatcgagtcggttaaaccagccaagtgtgtgctggaagacaaaaaatgggttgttgaatatcaacatggtaatcgtaacctggttatatctgacaccaacatcaggcagaccgtctacatctttaaatgtgacaactccacaatacaaatcaagggaaaagtcaactccatagccatggataattgtaagaagactgccttgctgtttgaagacgtcatctcgtcgtttgacgtcgttaattgtaacagcgtccaagcccaggtcacaggtaaaataaacactattaacattgacaagacagatggctgccaggtgtatttacaaag-ctccaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------catcctgacgtgcaccgcctcgatcctgaacctgtgcgcgatcgccatcgaccgctactacgccatacacgacccgatccggtacgcgcagaagcgcacgtgcaagcgcgtgctggtcagcatcgccctggtgtggctggtcagcgccctgatctcggtgccgccgctcgtcggctggaacaacagcggcggcaattcgctgtacaacgtcatctacagcgcgtcgggctcgttctacataccgctgctcatcatgacgttcgtctacttcaacatctttcgcgccacccggaagcggctgcgagcccgcgccaaggcggcggc------------cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
diff -r 000000000000 -r 961a712f9743 test-data/tree_model2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tree_model2 Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,1 @@
+(((Pg,Am) #$2,Th #3),(Ph,Ap)$1,Ac);
diff -r 000000000000 -r 961a712f9743 test-data/tree_model3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tree_model3 Tue Aug 29 19:12:01 2017 -0400
@@ -0,0 +1,1 @@
+(((Pg,Am),Th)$0,(Ph,Ap)$1,Ac);