acg-team · junniest · Nov 15, 2023 · Oct 10, 2023 · Oct 10, 2023 · Oct 10, 2023
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "git.ignoreLimitWarning": true
+}
diff --git a/phylo/data/Huelsenbeck_example.newick b/phylo/data/Huelsenbeck_example.newick
@@ -0,0 +1 @@
+((Species1:0.1,Species2:0.1):0.2,((Species3:0.1,Species4:0.1):0.1,Species5:0.2):0.1):0.0;
diff --git a/phylo/data/Huelsenbeck_example_long_DNA.fasta b/phylo/data/Huelsenbeck_example_long_DNA.fasta
@@ -0,0 +1,13 @@
+>Species2
+TGACTTTAAAGGACGACCCTACCAGGGCGGACACAAACGGACAGCGCAGC
+>Species4
+CGAGTTCAGAAGACGGCACCAACACAGCGGACGTATGCAGACGACGCACC
+>Species5
+TGCCCTTAGGAGGCGGCACTAACACCGCGGACGAGTGCGGACAACGTACC
+>Species1
+TAACTGTAAAGGACAACACTAGCAGGCCAGACGCACACGCACAGCGCACC
+>Species3
+CAAGTTTAGAAAACGGCACCAACACAACAGACGTATGCAACTGACGCACC
+
+
+
diff --git a/phylo/data/Huelsenbeck_example_reroot.newick b/phylo/data/Huelsenbeck_example_reroot.newick
@@ -0,0 +1 @@
+((Species5:0.20000000000000004,(Species1:0.10000000000000003,Species2:0.10000000000000003):0.30000000000000004):0.05,(Species3:0.10000000000000003,Species4:0.10000000000000003):0.05);
diff --git a/phylo/data/ambiguous_example.fasta b/phylo/data/ambiguous_example.fasta
@@ -0,0 +1,10 @@
+>orangutan
+XCCCCTCCCCTCATGTGTAC
+>chimp
+ACCCCTCCCCTCATGTGTAC
+>human
+ACCCCTCCCCTCATGTGTAC
+>gorilla
+ACCCCTCCCCTCATGTGTAC
+>unicorn
+TGCCCTCCCCTCATGTGTAC
diff --git a/phylo/data/ambiguous_example.newick b/phylo/data/ambiguous_example.newick
@@ -0,0 +1 @@
+(unicorn:15,(orangutan:13,(gorilla:10.25,(human:5.5,chimp:5.5):4.75):2.75):2);
diff --git a/phylo/data/ambiguous_example_N.fasta b/phylo/data/ambiguous_example_N.fasta
@@ -0,0 +1,10 @@
+>orangutan
+NCCCCTCCCCTCATGTGTAC
+>chimp
+ACCCCTCCCCTCATGTGTAC
+>human
+ACCCCTCCCCTCATGTGTAC
+>gorilla
+ACCCCTCCCCTCATGTGTAC
+>unicorn
+TGCCCTCCCCTCATGTGTAC
diff --git a/phylo/data/phyml_protein_example.fasta b/phylo/data/phyml_protein_example.fasta
@@ -0,0 +1,40 @@
+>Patas
+MASGILLNVKEEVTCPICLELLTEPLSLPCGHSFCQACITANHKKSMLYKEEERSCPVCRISYQPENIQPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDRKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVLADFEQLREILDWEESNELQYLEKEEEDILKSLTKSETKMVRQTQYVRELISDLEHRLQGSMMELLQGVDGIIKRIENMTLKKPETFHKNQRRVFRAPALKGMLDMFRELTDVRRYWVDVTLAPNNISHVVIAEDKRQVSSRNPQIMYWAQGKLF--------------------QSLKNFNYCTGILGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMYDVEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGVKYSVFQD-----------GSSHTPFAPFIAPLSVIFCPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>Colobus
+MASGILVNIKEEVTCPICLELLTEPLSLHCGHSFCQACITANHKKSMLYKEGERSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDRKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVLADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELVSDLEHRLQGSVMELLQGVDGIIKRIEDMTLKKPKTFPKNQRRVFRAPDLKGMLDMFRELTDVRRYWVDVTLAPNNISHAVIAEDKRRVSSPNPQIMYRAQGTLF--------------------QSLKNFIYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGVKYSVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>DLangur
+MASGILVNIKEEVTCPICLELLTEPLSLHCGHSFCQACITANHKKSMLYKEGERSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDRKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDCDKTNVLADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISDLEHRLQGSMMELLQGVDGIIKRIENMTLKKPKTFPKNQRRVFRAPDLKGILDMFRELTDVRRYWVDVTLAPNNISHAVIAEDKRQVSSPNPQIMCRARGTLF--------------------QSLKNFIYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGVKYNVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>AGM_cDNA
+MASGILVNVKEEVTCPICLELLTEPLSLPCGHSFCQACITANHKESMLYKEEERSCPVCRISYQPENIQPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISDLEHRLQGSMMELLQGVDGIIKRVENMTLKKPKTFHKNQRRVFRAPDLKGMLDMFRELTDVRRYWVDVTLAPNNISHAVIAEDKRQVSYRNPQIMYQSPGSLFGSLTNFSYCTGVPGSQSITSGKLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDATYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGDKYSVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>Tant_cDNA
+MASGILLNVKEEVTCPICLELLTEPLSLPCGHSFCQACITANHKESMLYKEEERSCPVCRISYQPENIQPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISDLEHRLQGSMMELLQGVDGIIKRIENMTLKKPKTFHKNQRRVFRAPDLKGMLDMFRELTDVRRYWVDVTLAPNNISHAVIAEDKRQVSYQNPQIMYQAPGSSFGSLTNFNYCTGVLGSQSITSRKLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDATYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGDKYSVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>Rhes_cDNA
+MASGILLNVKEEVTCPICLELLTEPLSLHCGHSFCQACITANHKKSMLYKEGERSCPVCRISYQPENIQPNRHVANIVEKLREVKLSPEEGQKVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIENMTLKKPKTFHKNQRRVFRAPDLKGMLDMFRELTDARRYWVDVTLATNNISHAVIAEDKRQVSSRNPQIMYQAPGTLF------------------TFPSLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQSDAMYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGVKYSVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>Baboon
+MASGILLNVKEEVTCPICLELLTEPLSLPCGHSFCQACITANHRKSMLYKEGERSCPVCRISYQPENIQPNRHVANIVEKLREVKLSPEEGLKVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISDLEHRLQGSMMELLQGVDGIIKRIENMTLKKPKTFHKNQRRVFRAPDLKGMLDMFRELTDVRRYWVDVTLAPNNISHAVIAEDKRQVSSRNPQITYQAPGTLF------------------SFPSLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLQEGVKYSVFQD-----------GSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVPMTLCSPSS
+>Gibbon
+MASGILVNVKEKVTCPICLELLTQPLSLDCGHSFCQACLTANHKTSMPDE-GERSCPVCRISYQHKNIRPNRHVANIVEKLREVKLSPEEGQKVDHCARHGKKLLLFCQEDRKVICWLCERSQEHRGHHTFLTEEVAQEYQMKLQAALQMLRQKQQEAEELEADIREEKASWKTQIQYDKTNILADFEQLRHILDWVESNELQNLEKEEKDVLKRLMRSEIEMVQQTQSVRELISDLEHRLQGSVMELLQGVDGVIKRMKNVTLKKPETFPKNRRRVFRAADLKVMLEVLRELRDVRRYWVDVTVAPNNISYAVISEDMRQVSSPEPQIIFEAQGTIS--------------------QTFVNFNYCTGILGSQSITSGKHYWEVDVSKKSAWILGVCAGLQPDAMYNIEQNENYQPKYGYWVI-------------------------------------------------------------GLEEGVKCNAFQD-----------GSIHTPSAPFVVPLSVNICPDRVGVFLDYEACTVSFFNITDHGFLIYKFSHCSFSQPVFPYLNPRKCTVPMTLCSPSS
+>Orangutan
+MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSTLDK-GERSCPVCRVSYQPKNIRPNRHVANIVEKLREVKLSPE-GQKVDHCARHGEKLLLFCKEDGKVICWLCERSQEHRGHHTFLTEEVAQKYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTSVLADFEQLRDILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQSVRELISDVEHRLQGSVMELLQGVDGIIKRMQNVTLKKPETFPKNQRRVFRAPNLKGMLEVFRELTDVRRYWVDVTVAPNDISYAVISEDMRQVSCPEPQIIYGAQGTTY--------------------QTYVNFNYCTGILGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMYNIEQNENYQPQYGYWVI-------------------------------------------------------------GLEEGVKCSAFQD-----------GSFHNPSAPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGFLIYKFSHCSFSQPVFPYLNPRKCRVPMTLCSPSS
+>Human
+MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDK-GESSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPE-GQKVDHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTNVLADFEQLRDILDWEESNELQNLEKEEEDILKSLTNSETEMVQQTQSLRELISDLEHRLQGSVMELLQGVDGVIKRTENVTLKKPETFPKNQRRVFRAPDLKGMLEVFRELTDVRRYWVDVTVAPNNISCAVISEDKRQVSSPKPQIIYGARGTRY--------------------QTFVNFNYCTGILGSQSITSGKHYWEVDVSKKTAWILGVCAGFQPDAMCNIEKNENYQPKYGYWVI-------------------------------------------------------------GLEEGVKCSAFQD-----------SSFHTPSVPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGFLIYKFSHCSFSQPVFPYLNPRKCGVPMTLCSPSS
+>Gorilla
+MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDK-GESSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPE-GQKVDHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAQEYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTNVLADFEQLRDILDWEESNELQNLEKEEEDILKRLTKSETEMVQQTQSVRELISDLEHRLQGSVMELLQGVDGVIKRMENVTLKKPETFPKNRRRVFRAPDLKGMLEVFRELTDVRRYWVDVTVAPNNISCAVISEDMRQVSSPKPQIIYGAQGTRY--------------------QTFMNFNYCTGILGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDATCNIEKNENYQPKYGYWVI-------------------------------------------------------------GLEEGVKCSAFQD-----------GSFHTPSAPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGFLIYKFSHCSFSQPVFPYLNPRKCRVPMTLCSPSS
+>Chimp
+MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDK-GESSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPE-GQKVDHCAHHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTNVLADFEQLRDILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQSVRELISDLERRLQGSVMELLQGVDGVIKRMENVTLKKPETFPKNQRRVFRAPDLKGMLEVFRELTDVRRYWVDVTVAPNNISCAVISEDMRQVSSPKPQIIYGARGTRY--------------------QTFMNFNYCTGILGSQSITSGKHYWEVDVSKKSAWILGVCAGFQPDAMCNIEKNENYQPKYGYWVI-------------------------------------------------------------GLEEGVKCSAFQD-----------GSFHTPSAPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGSLIYKFSHCSFSQPVFPYLNPRKCGVPMTLCSPSS
+>Squirrel
+MASRILGSIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESMLHQ-GERSCPLCRLPYQSENLRPNRHLASIVERLREVMLRPEERQNVDHCARHGEKLLLFCEQDGNIICWLCERSQEHRGHNTFLVEEVAQKYREKLQVALETMRQKQQDAEKLEADVRQEQASWKIQIQNDKTNIMAEFKQLRDILDCEESNELQNLEKEEKNILKRLVQSENDMVLQTQSVRVLISDLERRLQGSVVELLQDVDGVIKRIEKVTLQKPKTFLNEKRRVFRAPDLKRMLQVLKELTEVQRYWAHVTLVPSHPSYTIISEDGRQVRYQKPIR-----------------------------HLLVKVQYFYGVLGSPSITSGKHYWEVDVSNKRAWTLGVCVSLKCTANQSVSGTENYQPKNGYWVI-------------------------------------------------------------GLRNAGNYRAFQSSFEFR--DFLAGSRLTLSPPLIVPLFMTICPNRVGVFLDYEARTISFFNVTSNGFLIYKFSDCHFSYPVFPYFNPMTCELPMTLCSPRS
+>Howler
+MASKILVNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESR-----ERSCPLCRVSYHSENLRPNRHLANIAERLREVMLSPEEGQKVDRCARHGEKLLLFCQQHGNVICWLCERSEEHRGHRTSLVEEVAQKYREKLQAALEMMRQKEQDAEMLEADVREEQASWKIQIENDKTSTLAEFKQLRDILDCEESNELQKLEKEEENLLKRLVQSENDMVLQTQSIRVLIADLERRLQGSVMELLQGVEGVIKRIKNVTLQKPETFLNEKRRVFQAPDLKGMLQVFKELKEVQCYWAHVTLIPNHPSCTVISEDKREVRYQEQIHH----------------------------HPSMEVKYFYGILGSPSITSGKHYWEVDVSNKSAWILGVCVSLKCIG--NFPGIENYQPQNGYWVIGLRNADNYSAFQDAVPETENYQPKNRN-RFTGLQNADNCSAFQNAFPGIQSYQPKKSHLFTGLQNLSNYNAFQNKVQYNYIDFQDDSLSTPSAPLIVPLFMTICPKRVGVFLDYEACTVSFFNVTSNGYLIYKFSNCQFSYPVFPYFSPMTCELPMTLCSPSS
+>Spider
+MASEILLNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESTLHQ-GERSCPLCRVSYQSENLRPNRHLANIAERLREVMLSPEEGQKVDRCARHGEKLLLFCQQHGNVICWLCERSQEHRGHSTFLVEEVAQKYQEKLQVALEMMRQKQQDAEKLEADVREEQASWKIQIENDKTNILAEFKQLRDILDCEESNELQNLEKEEENLLKTLAQSENDMVLQTQSMRVLIADLEHRLQGSVMELLQDVEGVIKRIKNVTLQKPKTFLNEKRRVFRAPDLKGMLQVFKELKEVQCYWAHVTLVPSHPSCTVISEDERQVRYQEQIH-----------------------------QPSVKVKYFCGVLGSPGFTSGKHYWEVDVSDKSAWILGVCVSLKCTA--NVPGIENYQPKNGYWVIGLQNANNYSAFQDAVPGTENYQPKNGNRRNKGLRNADNYSAFRDTF------QPINDSWVTGLRNVDNYNAFQDAVKYS--DFQDGSCSTPSAPLMVPLFMTICPKRVGVFLDCKACTVSFFNVTSNGCLIYKFSKCHFSYPVFPYFSPMICKLPMTLCSPSS
+>Woolly
+MASEILVNIKEEVTCPICLDLLTEPLSLDCGHSFCQACITADHKESTLHQ-GERSCPLCRVGYQSENLRPNRHLANIAERLREVMLSPEEGQKVDRCARHGEKLLLFCQQHGNVICWLCERSQEHRGHSTFLVEEVAQKYREKLQVALEMMREKQQDAEKLEADVREEQASWKIQIKNDKTNILAEFKQLRDILDCEESNELQNLEKEEENLLKILAQSENDMVLQTQSMRVLIADLEHRLQGSVMELLQGVEGIIKRTTNVTLQKPKTFLNEKRRVFRAPNLKGMLQVFKELKEVQCYWAHVTLVPSHPSCAVISEDQRQVRYQKQRH-----------------------------RPSVKAKYFYGVLGSPSFTSGKHYWEVDVSNKSAWILGVCVSLKCTA--NVPGIENYQPKNGYWVIGLQNADNYSAFQDAVPGTEDYQPKNGCWRNTGLRNADNYSAFQDVF------QPKNDYWVTGLWNADNYNAFQDAGKYS--DFQDGSCSTPFAPLIVPLFMTIRPKRVGVFLDYEACTVSFFNVTSNGCLIYKFSNCHFSCPVFPYFSPMTCKLPMTLCSPSS
+>PMarmoset
+MASRILVNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESTLHQ-GERSCPLCRMSYPSENLRPNRHLANIVERLKEVMLSPEEGQKVDHCARHGEKLLLFCQQDGNVICWLCERSQEHRGHHTFLVEEVAEKYQGKLQVALEMMRQKQQDAEKLEADVREEQASWKIQIQNDKTNIMAEFKQLRDILDCEESKELQNLEKEEKNILKRLVQSESDMVLQTQSIRVLISDLERRLQGSVMELLQGVDDVIKRIEKVTLQKPKTFLNEKRRVFRAPDLKGMLQAFKELTEVQRYWAHVTLVPSHPSCTVISEDERQVRYQVPIH-----------------------------QPLVKVKYFYGVLGSLSITSGKHYWEVDVSNKRGWILGVCGSWKCNAKWNVLRPENYQPKNGYWVI-------------------------------------------------------------GLRNTDNYSAFQDAVKYS--DVQDGSRSVSSGPLIVPLFMTICPNRVGVFLDYEACTISFFNVTSNGFLIYKFSNCHFSYPVFPYFSPTTCELPMTLCSPSS
+>Tamarin
+MASRILVNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESTPHQ-GERSCPLCRMSYPSENLRPNRHLANIVERLKEVMLSPEEGQKVGHCARHGEKLLLFCEQDGNVICWLCERSQEHRGHHTLLVEEVAEKYQEKLQVALEMMRQKQQDAEKLEADVREEQASWKIQIRNDKTNIMAEFKQLRDILDCEESKELQNLEKEEKNILKRLVQSESDMVLQTQSMRVLISDLERRLQGSVLELLQGVDDVIKRIETVTLQKPKTFLNEKRRVFRAPDLKAMLQAFKELTEVQRYWAHVTLVPSHPSYAVISEDERQVRYQFQIH-----------------------------QPSVKVNYFYGVLGSPSITSGKHYWEVDVTNKRDWILGICVSFKCNAKWNVLRPENYQPKNGYWVI-------------------------------------------------------------GLQNTNNYSAFQDAVKYS--DFQIGSRSTASVPLIVPLFMTIYPNRVGVFLDYEACTVSFFNVTNNGFLIYKFSNCHFSYPVFPYFSPMTCELPMTLCSPSS
+>Titi
+MASRILVNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESTLHQ-GERSCPLCRISYPSENLRPNRHLANIVERLREVVLSPEEGQKVDLCARHGEKLLLFCQQDGNVICWLCERSQEHRGHHTFLVEEVAQTYRENLQVVLEMMRQKHQDAEKLEADVREEQASWKIQIQNDKTNIMAEFKQLRDILDCEESNELQNLEKEEKNILKRLVQSENDMVLQTQSISVLISDLEHRLQGSVMELLQGVDGVIKRVKNVTLQKPKTFLNEKRRVFRVPDLKGMLQVSKELTEVQRYWAHVTLVASHPSRAVISEDERQVRYQEWIH-----------------------------QSSGRVKYFYGVLGSPSITSGKHYWEVDVSNKSAWILGVCVSLKCAANRNGPGVENYQPKNGYWVI-------------------------------------------------------------GLRNADNYSAFQDSVKYN--DFQDGSRSTTYAPLIVPLFMTICPNRVGVFLDYEACTVSFFNVTSNGFLIYKFSNCHFSYPVFPYFSPMTCELPMTLCSPRS
+>Saki
+MASRILMNIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKKSMLHQ-GERSCPLCRISYPSENLRPNRHLANIVERLREVMLSPEEGQKVDHCARHGEKLLLFCQQDGNVICWLCERSQEHRGHHTLLVEEVAQTYRENLQVALETMRQKQQDAEKLEADVREEQASWKIQIRDDKTNIMAEFKQLRDILDCEESNELQILEKEEKNILKRLTQSENDMVLQTQSMGVLISDLEHRLQGSVMELLQGVDEVIKRVKNVTLQKPKTFLNEKRRVFRAPDLKGMLQVFKELTEVQRYWVHVTLVPSHLSCAVISEDERQVRYQERIH-----------------------------QSFGKVKYFYGVLGSPSIRSGKHYWEVDVSNKSAWILGVCVSLKCTANRNGPRIENYQPKNGYWVI-------------------------------------------------------------GLWNAGNYSAFQDSVKYS--DFQDGSHSATYGPLIVPLFMTICPNRVGVFLDYEACTVSFFNVTSNGFLIYKFSNCRFSDSVFPYFSPMTCELPMTLCSPRS
diff --git a/phylo/data/phyml_protein_example.newick b/phylo/data/phyml_protein_example.newick
@@ -0,0 +1 @@
+(((((((((Spider:0.03308191,Woolly:0.03582163):0.01444277,Howler:0.06799737):0.02909882,(((PMarmoset:0.02787360,Tamarin:0.03681352):0.01865025,Squirrel:0.08629746):0.01112128,(Saki:0.03881905,Titi:0.04068062):0.01757714):0.00607569):0.20818264,(((Chimp:0.01029099,Gorilla:0.00446741):0.00330774,Human:0.01513926):0.00720972,(Gibbon:0.05851278,Orangutan:0.03164833):0.00204286):0.02732959):0.04351306,(Colobus:0.00814254,DLangur:0.00661586):0.00733489):0.00608429,Patas:0.02612272):0.00687099,(AGM_cDNA:0.00495553,Tant_cDNA:0.00344975):0.00775707):0.00140317,Baboon:0.00482829):0.0,Rhes_cDNA:0.01205729):0.0;