From 3f61fc94aa28d1f45ce28129b197595607259d5d Mon Sep 17 00:00:00 2001 From: Brandon Invergo Date: Mon, 20 Feb 2012 13:00:33 +0100 Subject: [PATCH] Rearrange PAML test resource directory --- .../aa_alignment.phylip | 0 .../alignment.phylip | 0 .../lysinYangSwanson2002.nuc | 0 .../{Resources => Control_files}/README.txt | 0 Tests/PAML/{ => Control_files}/bad1.ctl | 0 Tests/PAML/{ => Control_files}/bad2.ctl | 0 Tests/PAML/{ => Control_files}/bad3.ctl | 0 .../baseml => Control_files}/baseml.ctl | 0 .../{ => Control_files/baseml}/baseml.ctl | 0 .../codeml/SE.ctl | 0 .../codeml/aa_model0.ctl | 0 .../codeml/aa_pairwise.ctl | 0 .../codeml/all_NSsites.ctl} | 0 .../codeml/branchsiteA.ctl | 0 .../codeml/clademodelC.ctl | 0 .../{ => Control_files/codeml}/codeml.ctl | 0 .../codeml/freeratio.ctl} | 0 .../codeml/ngene2_mgene012.ctl | 0 .../codeml/ngene2_mgene34.ctl | 0 .../codeml/pairwise.ctl | 0 .../{Resources => Control_files}/species.tree | 0 .../yn00 => Control_files}/yn00.ctl | 0 Tests/PAML/{ => Control_files/yn00}/yn00.ctl | 0 Tests/PAML/{ => Results}/bad_results.out | 0 .../codeml/{codeml_SE.out => SE/SE-4_3.out} | 0 .../aa_model0-4_4c.out} | 0 .../aa_pairwise-4_4c.out} | 0 .../all_NSsites-4_1.out} | 0 .../all_NSsites-4_3.out} | 0 .../all_NSsites-4_4.out} | 0 .../all_NSsites-4_4c.out} | 0 .../all_NSsites-4_5.out} | 0 .../branchsiteA-4_3.out} | 0 .../clademodelC-4_3.out} | 0 .../Results/codeml/codeml_NSsites_all.out | 429 ------------------ .../freeratio-4_4c.out} | 0 .../ngene2_mgene012-4_4c.out} | 0 .../ngene2_mgene34-4_4c.out} | 0 .../pairwise-4_4c.out} | 0 Tests/PAML/{ => Trees}/bad.tree | 0 .../{Resources/codeml => Trees}/lysin.trees | 0 Tests/PAML/{ => Trees}/species.tree | 0 Tests/PAML/aa_alignment.phylip | 16 - Tests/PAML/alignment.phylip | 31 -- 44 files changed, 476 deletions(-) rename Tests/PAML/{Resources => Alignments}/aa_alignment.phylip (100%) rename Tests/PAML/{Resources => Alignments}/alignment.phylip (100%) rename Tests/PAML/{Resources/codeml => Alignments}/lysinYangSwanson2002.nuc (100%) rename Tests/PAML/{Resources => Control_files}/README.txt (100%) rename Tests/PAML/{ => Control_files}/bad1.ctl (100%) mode change 100755 => 100644 rename Tests/PAML/{ => Control_files}/bad2.ctl (100%) rename Tests/PAML/{ => Control_files}/bad3.ctl (100%) rename Tests/PAML/{Resources/baseml => Control_files}/baseml.ctl (100%) mode change 100755 => 100644 rename Tests/PAML/{ => Control_files/baseml}/baseml.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/SE.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/aa_model0.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/aa_pairwise.ctl (100%) rename Tests/PAML/{Resources/codeml/allNSSites_and_allVersions.ctl => Control_files/codeml/all_NSsites.ctl} (100%) rename Tests/PAML/{Resources => Control_files}/codeml/branchsiteA.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/clademodelC.ctl (100%) rename Tests/PAML/{ => Control_files/codeml}/codeml.ctl (100%) rename Tests/PAML/{Resources/codeml/freebranch.ctl => Control_files/codeml/freeratio.ctl} (100%) rename Tests/PAML/{Resources => Control_files}/codeml/ngene2_mgene012.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/ngene2_mgene34.ctl (100%) rename Tests/PAML/{Resources => Control_files}/codeml/pairwise.ctl (100%) rename Tests/PAML/{Resources => Control_files}/species.tree (100%) rename Tests/PAML/{Resources/yn00 => Control_files}/yn00.ctl (100%) mode change 100755 => 100644 rename Tests/PAML/{ => Control_files/yn00}/yn00.ctl (100%) rename Tests/PAML/{ => Results}/bad_results.out (100%) rename Tests/PAML/Results/codeml/{codeml_SE.out => SE/SE-4_3.out} (100%) rename Tests/PAML/Results/codeml/{codeml_aa_model0.out => aa_model0/aa_model0-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{codeml_aa_pairwise.out => aa_pairwise/aa_pairwise-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{versions/codeml41.out => all_NSsites/all_NSsites-4_1.out} (100%) rename Tests/PAML/Results/codeml/{versions/codeml43.out => all_NSsites/all_NSsites-4_3.out} (100%) rename Tests/PAML/Results/codeml/{versions/codeml44.out => all_NSsites/all_NSsites-4_4.out} (100%) rename Tests/PAML/Results/codeml/{versions/codeml44c.out => all_NSsites/all_NSsites-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{versions/codeml45.out => all_NSsites/all_NSsites-4_5.out} (100%) rename Tests/PAML/Results/codeml/{codeml_branchsiteA.out => branchsiteA/branchsiteA-4_3.out} (100%) rename Tests/PAML/Results/codeml/{codeml_clademodelC.out => clademodelC/clademodelC-4_3.out} (100%) delete mode 100644 Tests/PAML/Results/codeml/codeml_NSsites_all.out rename Tests/PAML/Results/codeml/{codeml_freebranch.out => freeratio/freeratio-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{codeml_ngene2_mgene012.out => ngene2_mgene012/ngene2_mgene012-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{codeml_ngene2_mgene34.out => ngene2_mgene34/ngene2_mgene34-4_4c.out} (100%) rename Tests/PAML/Results/codeml/{codeml_pairwise.out => pairwise/pairwise-4_4c.out} (100%) rename Tests/PAML/{ => Trees}/bad.tree (100%) rename Tests/PAML/{Resources/codeml => Trees}/lysin.trees (100%) rename Tests/PAML/{ => Trees}/species.tree (100%) delete mode 100644 Tests/PAML/aa_alignment.phylip delete mode 100644 Tests/PAML/alignment.phylip diff --git a/Tests/PAML/Resources/aa_alignment.phylip b/Tests/PAML/Alignments/aa_alignment.phylip similarity index 100% rename from Tests/PAML/Resources/aa_alignment.phylip rename to Tests/PAML/Alignments/aa_alignment.phylip diff --git a/Tests/PAML/Resources/alignment.phylip b/Tests/PAML/Alignments/alignment.phylip similarity index 100% rename from Tests/PAML/Resources/alignment.phylip rename to Tests/PAML/Alignments/alignment.phylip diff --git a/Tests/PAML/Resources/codeml/lysinYangSwanson2002.nuc b/Tests/PAML/Alignments/lysinYangSwanson2002.nuc similarity index 100% rename from Tests/PAML/Resources/codeml/lysinYangSwanson2002.nuc rename to Tests/PAML/Alignments/lysinYangSwanson2002.nuc diff --git a/Tests/PAML/Resources/README.txt b/Tests/PAML/Control_files/README.txt similarity index 100% rename from Tests/PAML/Resources/README.txt rename to Tests/PAML/Control_files/README.txt diff --git a/Tests/PAML/bad1.ctl b/Tests/PAML/Control_files/bad1.ctl old mode 100755 new mode 100644 similarity index 100% rename from Tests/PAML/bad1.ctl rename to Tests/PAML/Control_files/bad1.ctl diff --git a/Tests/PAML/bad2.ctl b/Tests/PAML/Control_files/bad2.ctl similarity index 100% rename from Tests/PAML/bad2.ctl rename to Tests/PAML/Control_files/bad2.ctl diff --git a/Tests/PAML/bad3.ctl b/Tests/PAML/Control_files/bad3.ctl similarity index 100% rename from Tests/PAML/bad3.ctl rename to Tests/PAML/Control_files/bad3.ctl diff --git a/Tests/PAML/Resources/baseml/baseml.ctl b/Tests/PAML/Control_files/baseml.ctl old mode 100755 new mode 100644 similarity index 100% rename from Tests/PAML/Resources/baseml/baseml.ctl rename to Tests/PAML/Control_files/baseml.ctl diff --git a/Tests/PAML/baseml.ctl b/Tests/PAML/Control_files/baseml/baseml.ctl similarity index 100% rename from Tests/PAML/baseml.ctl rename to Tests/PAML/Control_files/baseml/baseml.ctl diff --git a/Tests/PAML/Resources/codeml/SE.ctl b/Tests/PAML/Control_files/codeml/SE.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/SE.ctl rename to Tests/PAML/Control_files/codeml/SE.ctl diff --git a/Tests/PAML/Resources/codeml/aa_model0.ctl b/Tests/PAML/Control_files/codeml/aa_model0.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/aa_model0.ctl rename to Tests/PAML/Control_files/codeml/aa_model0.ctl diff --git a/Tests/PAML/Resources/codeml/aa_pairwise.ctl b/Tests/PAML/Control_files/codeml/aa_pairwise.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/aa_pairwise.ctl rename to Tests/PAML/Control_files/codeml/aa_pairwise.ctl diff --git a/Tests/PAML/Resources/codeml/allNSSites_and_allVersions.ctl b/Tests/PAML/Control_files/codeml/all_NSsites.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/allNSSites_and_allVersions.ctl rename to Tests/PAML/Control_files/codeml/all_NSsites.ctl diff --git a/Tests/PAML/Resources/codeml/branchsiteA.ctl b/Tests/PAML/Control_files/codeml/branchsiteA.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/branchsiteA.ctl rename to Tests/PAML/Control_files/codeml/branchsiteA.ctl diff --git a/Tests/PAML/Resources/codeml/clademodelC.ctl b/Tests/PAML/Control_files/codeml/clademodelC.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/clademodelC.ctl rename to Tests/PAML/Control_files/codeml/clademodelC.ctl diff --git a/Tests/PAML/codeml.ctl b/Tests/PAML/Control_files/codeml/codeml.ctl similarity index 100% rename from Tests/PAML/codeml.ctl rename to Tests/PAML/Control_files/codeml/codeml.ctl diff --git a/Tests/PAML/Resources/codeml/freebranch.ctl b/Tests/PAML/Control_files/codeml/freeratio.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/freebranch.ctl rename to Tests/PAML/Control_files/codeml/freeratio.ctl diff --git a/Tests/PAML/Resources/codeml/ngene2_mgene012.ctl b/Tests/PAML/Control_files/codeml/ngene2_mgene012.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/ngene2_mgene012.ctl rename to Tests/PAML/Control_files/codeml/ngene2_mgene012.ctl diff --git a/Tests/PAML/Resources/codeml/ngene2_mgene34.ctl b/Tests/PAML/Control_files/codeml/ngene2_mgene34.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/ngene2_mgene34.ctl rename to Tests/PAML/Control_files/codeml/ngene2_mgene34.ctl diff --git a/Tests/PAML/Resources/codeml/pairwise.ctl b/Tests/PAML/Control_files/codeml/pairwise.ctl similarity index 100% rename from Tests/PAML/Resources/codeml/pairwise.ctl rename to Tests/PAML/Control_files/codeml/pairwise.ctl diff --git a/Tests/PAML/Resources/species.tree b/Tests/PAML/Control_files/species.tree similarity index 100% rename from Tests/PAML/Resources/species.tree rename to Tests/PAML/Control_files/species.tree diff --git a/Tests/PAML/Resources/yn00/yn00.ctl b/Tests/PAML/Control_files/yn00.ctl old mode 100755 new mode 100644 similarity index 100% rename from Tests/PAML/Resources/yn00/yn00.ctl rename to Tests/PAML/Control_files/yn00.ctl diff --git a/Tests/PAML/yn00.ctl b/Tests/PAML/Control_files/yn00/yn00.ctl similarity index 100% rename from Tests/PAML/yn00.ctl rename to Tests/PAML/Control_files/yn00/yn00.ctl diff --git a/Tests/PAML/bad_results.out b/Tests/PAML/Results/bad_results.out similarity index 100% rename from Tests/PAML/bad_results.out rename to Tests/PAML/Results/bad_results.out diff --git a/Tests/PAML/Results/codeml/codeml_SE.out b/Tests/PAML/Results/codeml/SE/SE-4_3.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_SE.out rename to Tests/PAML/Results/codeml/SE/SE-4_3.out diff --git a/Tests/PAML/Results/codeml/codeml_aa_model0.out b/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_aa_model0.out rename to Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4c.out diff --git a/Tests/PAML/Results/codeml/codeml_aa_pairwise.out b/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_aa_pairwise.out rename to Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4c.out diff --git a/Tests/PAML/Results/codeml/versions/codeml41.out b/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_1.out similarity index 100% rename from Tests/PAML/Results/codeml/versions/codeml41.out rename to Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_1.out diff --git a/Tests/PAML/Results/codeml/versions/codeml43.out b/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_3.out similarity index 100% rename from Tests/PAML/Results/codeml/versions/codeml43.out rename to Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_3.out diff --git a/Tests/PAML/Results/codeml/versions/codeml44.out b/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4.out similarity index 100% rename from Tests/PAML/Results/codeml/versions/codeml44.out rename to Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4.out diff --git a/Tests/PAML/Results/codeml/versions/codeml44c.out b/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/versions/codeml44c.out rename to Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4c.out diff --git a/Tests/PAML/Results/codeml/versions/codeml45.out b/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_5.out similarity index 100% rename from Tests/PAML/Results/codeml/versions/codeml45.out rename to Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_5.out diff --git a/Tests/PAML/Results/codeml/codeml_branchsiteA.out b/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_3.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_branchsiteA.out rename to Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_3.out diff --git a/Tests/PAML/Results/codeml/codeml_clademodelC.out b/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_3.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_clademodelC.out rename to Tests/PAML/Results/codeml/clademodelC/clademodelC-4_3.out diff --git a/Tests/PAML/Results/codeml/codeml_NSsites_all.out b/Tests/PAML/Results/codeml/codeml_NSsites_all.out deleted file mode 100644 index 4e47b48e0e0..00000000000 --- a/Tests/PAML/Results/codeml/codeml_NSsites_all.out +++ /dev/null @@ -1,429 +0,0 @@ - -seed used = 896544037 -CODONML (in paml version 4.3, August 2009) ../Tests/PAML/alignment.phylip -Model: One dN/dS ratio for branches -Codon frequency model: F3x4 -Site-class models: -ns = 5 ls = 74 - -Codon usage in sequences --------------------------------------------------------------------------------------------------- -Phe TTT 0 0 0 0 0 | Ser TCT 1 1 1 1 1 | Tyr TAT 0 0 1 0 0 | Cys TGT 3 2 3 3 3 - TTC 1 1 1 1 1 | TCC 1 1 1 1 1 | TAC 1 1 0 1 1 | TGC 0 1 0 0 0 -Leu TTA 0 0 0 0 0 | TCA 1 1 1 1 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 1 1 1 1 1 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Leu CTT 0 0 0 0 0 | Pro CCT 0 0 0 0 0 | His CAT 0 0 0 0 0 | Arg CGT 0 0 0 0 0 - CTC 2 2 2 2 2 | CCC 1 1 1 1 1 | CAC 0 0 0 0 0 | CGC 0 0 0 0 0 - CTA 1 1 1 1 1 | CCA 3 3 3 3 3 | Gln CAA 0 0 0 0 0 | CGA 1 1 1 1 1 - CTG 3 3 3 3 3 | CCG 0 0 0 0 0 | CAG 1 1 1 1 1 | CGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 2 2 2 2 2 | Thr ACT 0 0 0 0 0 | Asn AAT 2 2 2 2 2 | Ser AGT 0 0 0 0 0 - ATC 2 2 2 2 2 | ACC 0 0 0 0 0 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0 - ATA 0 0 0 0 0 | ACA 2 2 2 2 2 | Lys AAA 5 5 5 5 5 | Arg AGA 2 2 2 2 2 -Met ATG 3 3 3 3 3 | ACG 0 0 0 0 0 | AAG 5 5 5 5 5 | AGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Val GTT 3 3 3 3 1 | Ala GCT 0 0 0 0 0 | Asp GAT 2 2 2 2 2 | Gly GGT 0 0 0 0 0 - GTC 0 0 0 0 1 | GCC 0 0 0 0 0 | GAC 4 4 4 4 4 | GGC 3 3 3 3 3 - GTA 3 3 3 3 4 | GCA 0 0 0 0 0 | Glu GAA 8 8 8 8 8 | GGA 1 1 1 1 1 - GTG 2 2 2 2 2 | GCG 0 0 0 0 0 | GAG 4 4 4 4 4 | GGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: Homo_sapie -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676 -Average T:0.20270 C:0.16216 A:0.36937 G:0.26577 - -#2: Pan_troglo -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.16216 C:0.21622 A:0.36486 G:0.25676 -Average T:0.19820 C:0.16667 A:0.36937 G:0.26577 - -#3: Gorilla_go -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.18919 C:0.18919 A:0.36486 G:0.25676 -Average T:0.20721 C:0.15766 A:0.36937 G:0.26577 - -#4: Pongo_pygm -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676 -Average T:0.20270 C:0.16216 A:0.36937 G:0.26577 - -#5: Macaca_mul -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.14865 C:0.21622 A:0.37838 G:0.25676 -Average T:0.19369 C:0.16667 A:0.37387 G:0.26577 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 0 | Ser S TCT 5 | Tyr Y TAT 1 | Cys C TGT 14 - TTC 5 | TCC 5 | TAC 4 | TGC 1 -Leu L TTA 0 | TCA 5 | *** * TAA 0 | *** * TGA 0 - TTG 5 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 0 | Pro P CCT 0 | His H CAT 0 | Arg R CGT 0 - CTC 10 | CCC 5 | CAC 0 | CGC 0 - CTA 5 | CCA 15 | Gln Q CAA 0 | CGA 5 - CTG 15 | CCG 0 | CAG 5 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 10 | Thr T ACT 0 | Asn N AAT 10 | Ser S AGT 0 - ATC 10 | ACC 0 | AAC 0 | AGC 0 - ATA 0 | ACA 10 | Lys K AAA 25 | Arg R AGA 10 -Met M ATG 15 | ACG 0 | AAG 25 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 13 | Ala A GCT 0 | Asp D GAT 10 | Gly G GGT 0 - GTC 1 | GCC 0 | GAC 20 | GGC 15 - GTA 16 | GCA 0 | Glu E GAA 40 | GGA 5 - GTG 10 | GCG 0 | GAG 20 | GGG 0 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541 -position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514 -position 3: T:0.17027 C:0.20541 A:0.36757 G:0.25676 -Average T:0.20090 C:0.16306 A:0.37027 G:0.26577 - - -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.) - -Homo_sapie -Pan_troglo 0.0000 (0.0000 0.0207) -Gorilla_go 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421) -Pongo_pygm -1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0207) -Macaca_mul 0.0000 (0.0000 0.0421) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0421) - - -Model 0: one-ratio - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -lnL(ntime: 7 np: 9): -308.032819 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013437 0.013431 0.000004 0.027837 1.519173 0.000100 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013437): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027837); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013437): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027837); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51917 - -omega (dN/dS) = 0.00010 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0 - 7..8 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0 - 8..1 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0 - 8..2 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0 - 7..3 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0 - 6..4 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0 - 6..5 0.028 167.7 54.3 0.0001 0.0000 0.0379 0.0 2.1 - -tree length for dN: 0.0000 -tree length for dS: 0.0746 - - -Time used: 0:01 - - -Model 1: NearlyNeutral (2 categories) - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -lnL(ntime: 7 np: 10): -308.031692 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518329 0.999990 0.000001 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51833 - - -dN/dS (w) for site classes (K=2) - -p: 0.99999 0.00001 -w: 0.00000 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1 - - -Naive Empirical Bayes (NEB) analysis -Time used: 0:03 - - -Model 2: PositiveSelection (3 categories) - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -check convergence.. -lnL(ntime: 7 np: 12): -308.031579 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518235 1.000000 0.000000 0.000001 1.000000 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51824 - - -dN/dS (w) for site classes (K=3) - -p: 1.00000 0.00000 0.00000 -w: 0.00000 1.00000 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1 - - -Naive Empirical Bayes (NEB) analysis -Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) -Positively selected sites (*: P>95%; **: P>99%) -(amino acids refer to 1st sequence: Homo_sapie) - - Pr(w>1) post mean +- SE for w - - - - -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: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 - - -Posterior on the grid - -w0: 0.668 0.219 0.073 0.025 0.009 0.003 0.001 0.001 0.000 0.000 -w2: 0.281 0.168 0.120 0.093 0.076 0.065 0.057 0.051 0.046 0.043 - -Posterior for p0-p1 (see the ternary graph) - - 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 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.020 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.004 0.014 0.058 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.004 0.011 0.040 0.168 - 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 0.002 0.005 0.012 0.033 0.118 0.484 - -sum of density on p0-p1 = 1.000000 - -Time used: 0:15 - - -Model 3: discrete (3 categories) - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -lnL(ntime: 7 np: 13): -308.031579 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518247 0.366397 0.431592 0.000001 0.000001 0.000001 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51825 - - -dN/dS (w) for site classes (K=3) - -p: 0.36640 0.43159 0.20201 -w: 0.00000 0.00000 0.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0 - 6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0 - 6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1 - - -Naive Empirical Bayes (NEB) analysis -Time used: 0:18 - - -Model 7: beta (10 categories) - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -lnL(ntime: 7 np: 10): -308.031567 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518220 0.005000 99.000000 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51822 - -Parameters in M7 (beta): - p= 0.00500 q= 99.00000 - - -dN/dS (w) for site classes (K=10) - -p: 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 -w: 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 7..8 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 8..1 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 8..2 0.013 167.7 54.3 -nan -nan 0.0169 -nan 0.9 - 7..3 0.013 167.7 54.3 -nan -nan 0.0169 -nan 0.9 - 6..4 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 6..5 0.028 167.7 54.3 -nan -nan 0.0351 -nan 1.9 - - -Naive Empirical Bayes (NEB) analysis -Time used: 0:58 - - -Model 8: beta&w>1 (11 categories) - - -TREE # 1: (((1, 2), 3), 4, 5); MP score: 4 -lnL(ntime: 7 np: 12): -308.031680 +0.000000 - 6..7 7..8 8..1 8..2 7..3 6..4 6..5 - 0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518312 0.999990 0.005000 99.000000 1.000000 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.05472 - -(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839); - -(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839); - -Detailed output identifying parameters - -kappa (ts/tv) = 1.51831 - -Parameters in M8 (beta&w>1): - p0= 0.99999 p= 0.00500 q= 99.00000 - (p1= 0.00001) w= 1.00000 - - -dN/dS (w) for site classes (K=11) - -p: 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.00001 -w: 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 7..8 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 8..1 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 8..2 0.013 167.7 54.3 -nan -nan 0.0169 -nan 0.9 - 7..3 0.013 167.7 54.3 -nan -nan 0.0169 -nan 0.9 - 6..4 0.000 167.7 54.3 -nan -nan 0.0000 -nan 0.0 - 6..5 0.028 167.7 54.3 -nan -nan 0.0351 -nan 1.9 - - -Naive Empirical Bayes (NEB) analysis -Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) -Positively selected sites (*: P>95%; **: P>99%) -(amino acids refer to 1st sequence: Homo_sapie) - - Pr(w>1) post mean +- SE for w - - - - -The grid - -p0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 -p : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900 -q : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900 -ws: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 - - -Posterior on the grid - -p0: 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.014 0.082 0.899 -p : 0.628 0.200 0.082 0.039 0.021 0.012 0.007 0.005 0.003 0.002 -q : 0.001 0.015 0.037 0.061 0.086 0.111 0.136 0.160 0.184 0.209 -ws: 0.332 0.183 0.122 0.088 0.068 0.055 0.046 0.040 0.035 0.031 - -Time used: 1:54 - -Time used: 1:54 diff --git a/Tests/PAML/Results/codeml/codeml_freebranch.out b/Tests/PAML/Results/codeml/freeratio/freeratio-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_freebranch.out rename to Tests/PAML/Results/codeml/freeratio/freeratio-4_4c.out diff --git a/Tests/PAML/Results/codeml/codeml_ngene2_mgene012.out b/Tests/PAML/Results/codeml/ngene2_mgene012/ngene2_mgene012-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_ngene2_mgene012.out rename to Tests/PAML/Results/codeml/ngene2_mgene012/ngene2_mgene012-4_4c.out diff --git a/Tests/PAML/Results/codeml/codeml_ngene2_mgene34.out b/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_ngene2_mgene34.out rename to Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4c.out diff --git a/Tests/PAML/Results/codeml/codeml_pairwise.out b/Tests/PAML/Results/codeml/pairwise/pairwise-4_4c.out similarity index 100% rename from Tests/PAML/Results/codeml/codeml_pairwise.out rename to Tests/PAML/Results/codeml/pairwise/pairwise-4_4c.out diff --git a/Tests/PAML/bad.tree b/Tests/PAML/Trees/bad.tree similarity index 100% rename from Tests/PAML/bad.tree rename to Tests/PAML/Trees/bad.tree diff --git a/Tests/PAML/Resources/codeml/lysin.trees b/Tests/PAML/Trees/lysin.trees similarity index 100% rename from Tests/PAML/Resources/codeml/lysin.trees rename to Tests/PAML/Trees/lysin.trees diff --git a/Tests/PAML/species.tree b/Tests/PAML/Trees/species.tree similarity index 100% rename from Tests/PAML/species.tree rename to Tests/PAML/Trees/species.tree diff --git a/Tests/PAML/aa_alignment.phylip b/Tests/PAML/aa_alignment.phylip deleted file mode 100644 index 0ae1f1e61cd..00000000000 --- a/Tests/PAML/aa_alignment.phylip +++ /dev/null @@ -1,16 +0,0 @@ ->Homo_sapie ---MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS -GEDPLVKGIPEDKNPFKELKGGCVIS--------------- ->Pan_troglo ---MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS -GEDPLVKGIPEDKNPFKELKGGCVIS--------------- ->Gorilla_go -KKMPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS -GEDPLVKGIPEDKNPFKELKGGCVIS--------------- ->Pongo_pygm ---MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS -GEDPLVKGIPEDKNPFKELKGGCVIS--------------- ->Macaca_mul ---MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS -GEDPLVKGIPEDKNPFKELKGGCVISKYRKKILNCWKYLKC - diff --git a/Tests/PAML/alignment.phylip b/Tests/PAML/alignment.phylip deleted file mode 100644 index 4d6662d10cb..00000000000 --- a/Tests/PAML/alignment.phylip +++ /dev/null @@ -1,31 +0,0 @@ - 5 222 I -Homo_sapie ATGCCAGTAA TCAATATTGA GGACCTGACA GAAAAGGACA AATTGAAGAT -Pan_troglo ATGCCAGTAA TCAATATTGA GGACCTGACA GAAAAGGACA AATTGAAGAT -Gorilla_go ATGCCAGTAA TCAATATTGA GGACCTGACA GAAAAGGACA AATTGAAGAT -Pongo_pygm ATGCCAGTAA TCAATATTGA GGACCTGACA GAAAAGGACA AATTGAAGAT -Macaca_mul ATGCCAGTAA TCAATATTGA GGACCTGACA GAAAAGGACA AATTGAAGAT - - GGAAGTTGAC CAGCTCAAGA AAGAAGTGAC ACTGGAAAGA ATGCTAGTTT - GGAAGTTGAC CAGCTCAAGA AAGAAGTGAC ACTGGAAAGA ATGCTAGTTT - GGAAGTTGAC CAGCTCAAGA AAGAAGTGAC ACTGGAAAGA ATGCTAGTTT - GGAAGTTGAC CAGCTCAAGA AAGAAGTGAC ACTGGAAAGA ATGCTAGTTT - GGAAGTTGAC CAGCTCAAGA AAGAAGTGAC ACTGGAAAGA ATGCTAGTAT - - CCAAATGTTG TGAAGAAGTA AGAGATTACG TTGAAGAACG ATCTGGCGAG - CCAAATGCTG TGAAGAAGTA AGAGATTACG TTGAAGAACG ATCTGGCGAG - CCAAATGTTG TGAAGAAGTA AGAGATTATG TTGAAGAACG ATCTGGCGAG - CCAAATGTTG TGAAGAAGTA AGAGATTACG TTGAAGAACG ATCTGGCGAG - CCAAATGTTG TGAAGAAGTA AGAGATTACG TCGAAGAACG ATCTGGCGAG - - GATCCACTGG TAAAGGGCAT CCCAGAGGAC AAAAATCCCT TCAAGGAGCT - GATCCACTGG TAAAGGGCAT CCCAGAGGAC AAAAATCCCT TCAAGGAGCT - GATCCACTGG TAAAGGGCAT CCCAGAGGAC AAAAATCCCT TCAAGGAGCT - GATCCACTGG TAAAGGGCAT CCCAGAGGAC AAAAATCCCT TCAAGGAGCT - GATCCACTGG TAAAGGGCAT CCCAGAGGAC AAAAATCCCT TCAAGGAGCT - - CAAAGGAGGC TGTGTGATTT CATGA - CAAAGGAGGC TGTGTGATTT CATGA - CAAAGGAGGC TGTGTGATTT CATGA - CAAAGGAGGC TGTGTGATTT CATGA - CAAAGGAGGC TGTGTGATTT CATGA -