Mercurial > repos > iuc > pal2nal

annotate test-data/inputs/for_paml/test.codeml.ori @ 0:a14d5c1e1fc4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:21 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
1 CODONML (in paml 3.14, March 2005) test.codon Model: several dN/dS ratios for branches
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
2 Codon frequencies: F3x4
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
3
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
4 ns = 2 ls = 177
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
5 # site patterns = 105
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
6 2 1 1 1 1 1 1 1 1 1 4 3 2 1 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
7 1 1 4 1 1 2 1 1 1 7 2 3 1 2 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
8 2 1 3 1 1 2 2 8 1 1 1 1 1 1 7
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
9 1 1 1 3 1 4 1 1 4 1 1 3 2 1 6
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
10 1 1 1 2 1 1 1 6 2 1 3 1 1 4 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
11 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
12 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
13
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
14
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
15 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
16 BC070280 CTA AAC TGC ATC GTC GCT GTG TCC CAG AAC ATG GGC ATC GGC AAG AAC GGG GAC CTG CCC CCA CCG CTC AGG AAT GAA TTC CAG AGA ACC ACA ACC TCT TCA GTA GAA GGT AAA CAG CTG GTG ATT ATG GGT AAG ACC TGG TCC ATT CCT GAG CGA CCT TTA GGT AGA GTT CTC AGC GAA CTC CCT CCA CAA GGA GCT CAT TTT CTT TCC AGT CTA GAT GAT GCC CTT ACT CCA GCA GTA ATG CTC TGG ATA GTT GGT TAT GCC GGC CAT CTT GTG AGG CAA GAA ACG ATT TTG CTG CCA TAC GTC CAG GTA GAG
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
17 pseudogene ... ... ... ..T ... AA. .AT ... ... ..G ... ... ... AT. .G. ..T ... ... ... ... ..T .A. ... .AA ... A.. ... ..A ... ... ... C.. ... ... .C. ..G ... ... G.A T.A ..A T.. T.A AT. ... .A. ... ..G ... A.. ... .A. ... ... TA. .T. ... G.. ..T ... TC. ..A ..G ... A.. C.. .C. ... ... GA. ... ..G .G. ... ... .G. .T. .T. ... CA. G.. T.T .TT .C. ..G ..A ... T.. .A. ... T.. ... T.. ..G C.. ... GG. ..A ..C ... ... ..G G.. ... ..A
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
18
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
19 Codon usage in sequences
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
20 --------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
21 Phe TTT 6 10 | Ser TCT 3 3 | Tyr TAT 3 4 | Cys TGT 0 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
22 TTC 3 3 | TCC 3 3 | TAC 2 2 | TGC 1 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
23 Leu TTA 4 7 | TCA 1 1 | *** TAA 0 0 | *** TGA 0 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
24 TTG 1 0 | TCG 0 1 | TAG 0 0 | Trp TGG 2 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
25 --------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
26 Leu CTT 4 2 | Pro CCT 3 5 | His CAT 2 1 | Arg CGT 0 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
27 CTC 5 2 | CCC 1 2 | CAC 0 0 | CGC 0 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
28 CTA 3 3 | CCA 6 3 | Gln CAA 3 6 | CGA 1 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
29 CTG 3 2 | CCG 1 1 | CAG 4 3 | CGG 0 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
30 --------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
31 Ile ATT 5 6 | Thr ACT 1 1 | Asn AAT 7 9 | Ser AGT 3 4
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
32 ATC 3 3 | ACC 3 1 | AAC 3 2 | AGC 1 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
33 ATA 1 1 | ACA 2 3 | Lys AAA 8 11 | Arg AGA 3 3
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
34 Met ATG 6 4 | ACG 1 1 | AAG 9 8 | AGG 2 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
35 --------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
36 Val GTT 4 3 | Ala GCT 2 0 | Asp GAT 5 5 | Gly GGT 5 4
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
37 GTC 2 3 | GCC 2 1 | GAC 4 6 | GGC 5 3
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
38 GTA 3 2 | GCA 1 2 | Glu GAA 11 8 | GGA 1 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
39 GTG 3 4 | GCG 0 0 | GAG 5 7 | GGG 1 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
40 --------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
41
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
42 Codon position x base (3x4) table for each sequence.
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
43
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
44 #1: BC070280
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
45 position 1: T:0.16384 C:0.20339 A:0.32768 G:0.30508
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
46 position 2: T:0.31638 C:0.16949 A:0.37288 G:0.14124
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
47 position 3: T:0.29944 C:0.21469 A:0.27119 G:0.21469
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
48
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
49 #2: pseudogene
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
50 position 1: T:0.20904 C:0.17514 A:0.33333 G:0.28249
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
51 position 2: T:0.31073 C:0.15819 A:0.40678 G:0.12429
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
52 position 3: T:0.32768 C:0.18079 A:0.28814 G:0.20339
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
53
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
54 Sums of codon usage counts
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
55 ------------------------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
56 Phe F TTT 16 | Ser S TCT 6 | Tyr Y TAT 7 | Cys C TGT 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
57 TTC 6 | TCC 6 | TAC 4 | TGC 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
58 Leu L TTA 11 | TCA 2 | *** * TAA 0 | *** * TGA 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
59 TTG 1 | TCG 1 | TAG 0 | Trp W TGG 4
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
60 ------------------------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
61 Leu L CTT 6 | Pro P CCT 8 | His H CAT 3 | Arg R CGT 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
62 CTC 7 | CCC 3 | CAC 0 | CGC 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
63 CTA 6 | CCA 9 | Gln Q CAA 9 | CGA 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
64 CTG 5 | CCG 2 | CAG 7 | CGG 0
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
65 ------------------------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
66 Ile I ATT 11 | Thr T ACT 2 | Asn N AAT 16 | Ser S AGT 7
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
67 ATC 6 | ACC 4 | AAC 5 | AGC 1
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
68 ATA 2 | ACA 5 | Lys K AAA 19 | Arg R AGA 6
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
69 Met M ATG 10 | ACG 2 | AAG 17 | AGG 4
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
70 ------------------------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
71 Val V GTT 7 | Ala A GCT 2 | Asp D GAT 10 | Gly G GGT 9
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
72 GTC 5 | GCC 3 | GAC 10 | GGC 8
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
73 GTA 5 | GCA 3 | Glu E GAA 19 | GGA 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
74 GTG 7 | GCG 0 | GAG 12 | GGG 2
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
75 ------------------------------------------------------------------------------
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
76
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
77
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
78 Codon position x base (3x4) table, overall
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
79
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
80 position 1: T:0.18644 C:0.18927 A:0.33051 G:0.29379
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
81 position 2: T:0.31356 C:0.16384 A:0.38983 G:0.13277
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
82 position 3: T:0.31356 C:0.19774 A:0.27966 G:0.20904
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
83
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
84
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
85 Nei & Gojobori 1986. dN/dS (dN, dS)
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
86 (Note: This matrix is not used in later m.l. analysis.
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
87 Use runmode = -2 for ML pairwise comparison.)
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
88
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
89 BC070280
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
90 pseudogene 0.5224 (0.1421 0.2721)
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
91
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
92 pairwise comparison, codon frequencies: F3x4.
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
93
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
94
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
95 2 (pseudogene) ... 1 (BC070280)
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
96 lnL =-1014.258355
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
97 0.52723 1.94064 0.59797
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
98
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
99 t= 0.5272 S= 129.6 N= 401.4 dN/dS= 0.5980 dN= 0.1510 dS= 0.2525
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
100
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
101
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
parents:
diff changeset
102