Mercurial > repos > iuc > pal2nal
diff test-data/inputs/for_paml/test.codeml.ori @ 0:a14d5c1e1fc4 draft default tip
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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/for_paml/test.codeml.ori Sun Nov 09 10:56:21 2025 +0000 @@ -0,0 +1,102 @@ +CODONML (in paml 3.14, March 2005) test.codon Model: several dN/dS ratios for branches +Codon frequencies: F3x4 + +ns = 2 ls = 177 +# site patterns = 105 + 2 1 1 1 1 1 1 1 1 1 4 3 2 1 2 + 1 1 4 1 1 2 1 1 1 7 2 3 1 2 1 + 2 1 3 1 1 2 2 8 1 1 1 1 1 1 7 + 1 1 1 3 1 4 1 1 4 1 1 3 2 1 6 + 1 1 1 2 1 1 1 6 2 1 3 1 1 4 1 + 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 + 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 + + +1 +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 +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 + +Codon usage in sequences +-------------------------------------------------------------- +Phe TTT 6 10 | Ser TCT 3 3 | Tyr TAT 3 4 | Cys TGT 0 0 + TTC 3 3 | TCC 3 3 | TAC 2 2 | TGC 1 1 +Leu TTA 4 7 | TCA 1 1 | *** TAA 0 0 | *** TGA 0 0 + TTG 1 0 | TCG 0 1 | TAG 0 0 | Trp TGG 2 2 +-------------------------------------------------------------- +Leu CTT 4 2 | Pro CCT 3 5 | His CAT 2 1 | Arg CGT 0 1 + CTC 5 2 | CCC 1 2 | CAC 0 0 | CGC 0 0 + CTA 3 3 | CCA 6 3 | Gln CAA 3 6 | CGA 1 0 + CTG 3 2 | CCG 1 1 | CAG 4 3 | CGG 0 0 +-------------------------------------------------------------- +Ile ATT 5 6 | Thr ACT 1 1 | Asn AAT 7 9 | Ser AGT 3 4 + ATC 3 3 | ACC 3 1 | AAC 3 2 | AGC 1 0 + ATA 1 1 | ACA 2 3 | Lys AAA 8 11 | Arg AGA 3 3 +Met ATG 6 4 | ACG 1 1 | AAG 9 8 | AGG 2 2 +-------------------------------------------------------------- +Val GTT 4 3 | Ala GCT 2 0 | Asp GAT 5 5 | Gly GGT 5 4 + GTC 2 3 | GCC 2 1 | GAC 4 6 | GGC 5 3 + GTA 3 2 | GCA 1 2 | Glu GAA 11 8 | GGA 1 1 + GTG 3 4 | GCG 0 0 | GAG 5 7 | GGG 1 1 +-------------------------------------------------------------- + +Codon position x base (3x4) table for each sequence. + +#1: BC070280 +position 1: T:0.16384 C:0.20339 A:0.32768 G:0.30508 +position 2: T:0.31638 C:0.16949 A:0.37288 G:0.14124 +position 3: T:0.29944 C:0.21469 A:0.27119 G:0.21469 + +#2: pseudogene +position 1: T:0.20904 C:0.17514 A:0.33333 G:0.28249 +position 2: T:0.31073 C:0.15819 A:0.40678 G:0.12429 +position 3: T:0.32768 C:0.18079 A:0.28814 G:0.20339 + +Sums of codon usage counts +------------------------------------------------------------------------------ +Phe F TTT 16 | Ser S TCT 6 | Tyr Y TAT 7 | Cys C TGT 0 + TTC 6 | TCC 6 | TAC 4 | TGC 2 +Leu L TTA 11 | TCA 2 | *** * TAA 0 | *** * TGA 0 + TTG 1 | TCG 1 | TAG 0 | Trp W TGG 4 +------------------------------------------------------------------------------ +Leu L CTT 6 | Pro P CCT 8 | His H CAT 3 | Arg R CGT 1 + CTC 7 | CCC 3 | CAC 0 | CGC 0 + CTA 6 | CCA 9 | Gln Q CAA 9 | CGA 1 + CTG 5 | CCG 2 | CAG 7 | CGG 0 +------------------------------------------------------------------------------ +Ile I ATT 11 | Thr T ACT 2 | Asn N AAT 16 | Ser S AGT 7 + ATC 6 | ACC 4 | AAC 5 | AGC 1 + ATA 2 | ACA 5 | Lys K AAA 19 | Arg R AGA 6 +Met M ATG 10 | ACG 2 | AAG 17 | AGG 4 +------------------------------------------------------------------------------ +Val V GTT 7 | Ala A GCT 2 | Asp D GAT 10 | Gly G GGT 9 + GTC 5 | GCC 3 | GAC 10 | GGC 8 + GTA 5 | GCA 3 | Glu E GAA 19 | GGA 2 + GTG 7 | GCG 0 | GAG 12 | GGG 2 +------------------------------------------------------------------------------ + + +Codon position x base (3x4) table, overall + +position 1: T:0.18644 C:0.18927 A:0.33051 G:0.29379 +position 2: T:0.31356 C:0.16384 A:0.38983 G:0.13277 +position 3: T:0.31356 C:0.19774 A:0.27966 G:0.20904 + + +Nei & Gojobori 1986. dN/dS (dN, dS) +(Note: This matrix is not used in later m.l. analysis. +Use runmode = -2 for ML pairwise comparison.) + +BC070280 +pseudogene 0.5224 (0.1421 0.2721) + +pairwise comparison, codon frequencies: F3x4. + + +2 (pseudogene) ... 1 (BC070280) +lnL =-1014.258355 + 0.52723 1.94064 0.59797 + +t= 0.5272 S= 129.6 N= 401.4 dN/dS= 0.5980 dN= 0.1510 dS= 0.2525 + + +