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cogent3 / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
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Construct a minimal sample sequence alignment between 3 taxa using cogent3 #12

Closed khiron closed 1 year ago

khiron commented 1 year ago

Create \tests\data\three-ungapped.fa using cogent3 to use as test data to compare cogent3 maximum likelihood results with iqtree2 in #10 

>Human
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGTTTATTACTCACTAAA
GACAGAATGAATGTAGAAAAGGCTGAATTCTGTAATAAAAGCAAACAGCCTGGCTTAGCA
AGGAGCCAACATAACAGATGGGCTGGAAGTAAGGAAACATGTAATGATAGGCGGACTCCC
AGCACAGAAAAAAAGGTAGATCTGAATGCTGATCCCCTGTGTGAGAGAAAAGAATGGAAT
AAGCAGAAACTGCCATGCTCAGAGAATCCTAGAGATACTGAAGATGTTCCTTGGATAACA
CTAAATAGCAGCATTCAGAAAGTTAATGAGTGGTTTTCCAGAAGTGATGAACTGTTAGGT
TCTGATGACTCACATGATGGGGAGTCTGAATCAAATGCCAAAGTAGCTGATGTATTGGAC
GTTCTAAATGAGGTAGATGAATATTCTGGTTCTTCAGAGAAAATAGACTTACTGGCCAGT
GATCCTCATGAGGCTTTAATATGTAAAAGTGAAAGAGTTCACTCCAAATCAGTAGAGAGT
AATATTGAAGACAAAATATTTGGGAAAACCTATCGGAAGAAGGCAAGCCTCCCCAACTTA
AGCCATGTAACTGAAATTATAGGAGCATTTGTTACTGAGCCACAGATAATACAAGAGCGT
CCCCTCACAAATAAATTAAAGCGTAAAAGGACATCAGGCCTTCATCCTGAGGATTTTATC
AAGAAAGCAGATTTGGCAGTTCAAAAGACTCCTGAAATGATAAATCAGGGAACTAACCAA
ACGGAGCAGAATGGTCAAGTGATGAATATTACTAATAGTGGTCATGAGAATAAAACAAAA
GGTGATTCTATTCAGAATGAGAAAAATCCTAACCCAATAGAATCACTCGAAAAAGAATCT
GCTTTCAAAACGAAAGCTGAACCTATAAGCAGCAGTATAAGCAATATGGAACTCGAATTA
AATATCCACAATTCAAAAGCACCTAAAAAGAATAGGCTGAGGAGGAAGTCTTCTACCAGG
CATATTCATGCGCTTGAACTAGTCAGTAGAAATCTAAGCCCACCTAATTGTACTGAATTG
CAAATTGATAGTTGTTCTAGCAGTGAAGAGATAAAGAAAAAAAAGTACAACCAAATGCCA
GTCAGGCACAGCAGAAACCTACAACTCATGGAAGGTAAAGAACCTGCAACTGGAGCCAAG
AAGAACAAGCCAAATGAACAGACAAGTAAAAGACATGACAGCGATACTTTCCCAGAGCTG
AAGTTAACAAATGCACCTGGTTCTTTTACTAAGTGTTCAAATACCAGTGAAAAAGAATTT
GTCAATCCTAGCCTTCCAAGAGAAGAAAAAGAGAAACTAGAAACAGTTAAAGTGTCTAAT
AATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAGAAAGGGTTTTGCAAACTGAAAGA
TCTGTAGAGAGTAGCAGTATTTCATTGGTACCTGGTACTGATTATGGCACTCAGGAAAGT
ATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGTGTG
AGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTCCAAAGATAATAGA
AATGACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACA
ATAGAAATGGAAGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCA
AAGCGCCAGTCATTTGCTCCGTTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCACAC
TCTGGGTCCTTAAAGAAACAAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAAAT
CAAGGAAAGAATGAGTCTAATATCAAGCCTGTACAGACAGTTAATATCACTGCAGGCTTT
CCTGTGGTTGGTCAGAAAGATAAGCCAGTTGATAATGCCAAATGTAAAGGAGGCTCTAGG
TTTTGTCTATCATCTCAGTTCAGAGGCAACGAAACTGGACTCATTACTCCAAATAAACAT
GGACTTTTACAAAACCCATATCGTATACCACCACTTTTTCCCATCAAGTCATTTGTTAAA
ACTAAATGTAAGAAAAATCTGCTAGAGGAAAACTTTGAGGAACATTCAATGTCACCTGAA
AGAGAAATGGGAAATGAGAACATTCCAAGTACAGTGAGCACAATTAGCCGTAATAACAGA
GAAAATGTTTTTAAAGAAGCCAGCTCAAGCAATATTAATGAAGTAGGTTCCAGTGATGAA
AACATTCAAGCAGAACTAGGTAGAAACAGAGGGCCAAAATTGAATGCTATGCTTAGATTA
GGGGTTTTGCAACCTGAGGTCTATAAACAAAGTCTTCCTGGAAGTAATAAGCATCCTGAA
ATAAAAAAGCAAGAAGTTCAGACTGTTAATACAGATTTCTCTCCATATCTGATTTCAGAT
AACTTAGAACAGCCTATGAGTAGTCATGCATCTCAGGTTTGTTCTGAGACACCTGATGAC
CTGTTAGATGATGGTGAAATAAAGGAAGATACTAGTTTTGCTGAAAATGACATTAAGGAA
AGTTCTGCTGTTTTTAGCAAAAGCGTCCAGAAAGGAGAGCTTAGCAGGAGTCCTAGCCCT
TTCACCCATACACATTTGGCTCAGGGTTACCGAAGAGGGGCCAAGAAATTAGAGTCCTCA
GAAGAGAACTTATCTAGTGAG
>Rhesus
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGTTTGTTACTCACTAAA
GACAGAATGAATGTAGAAAAGGCTGAATTCTGTAATAAAAGCAAACAGCCTGGCTTGGCA
AGGAGCCAACATAACAGATGGACTGGAAGTAAGGAAACATGTAATGATAGGCAGACTCCC
AGCACAGAGAAAAAGGTAGATCTGAATGCTAATGCCCTGTATGAGAGAAAAGAATGGAAT
AAGCAAAAACTGCCATGCTCTGAGAATCCTAGAGACACTGAAGATGTTCCTTGGATAACA
CTAAATAGCAGCATTCAGAAAGTTAATGAGTGGTTTTCCAGAAGTGATGAACTGTTAAGT
TCTGATGACTCACATGATGGGGGGTCTGAATCAAATGCCAAAGTAGCTGATGTATTGGAC
GTTCTAAATGAGGTAGATGAATATTCTGGTTCTTCAGAGAAAATAGACTTACTGGCCAGT
GATCCTCATGAGCCTTTAATATGTAAAAGTGAAAGAGTTCACTCCAGTTCAGTAGAGAGT
AATATTAAAGACAAAATATTTGGGAAAACCTATCGGAGGAAGGCAAACCTTCCCAATTTA
AGCCATGTAACTGAAATTATAGGAGCACTTGTTACTGAGTCACAGATAATGCAAGAGCGT
CCCCTCACAAATAAATTAAAGCGTAAAAGGACATCAGGTCTTCATCCTGAGGATTTTATA
AAGAAAGCAGATTTGGCAGTTCAAAAGACTCCTGAAATAATAAATCAGGGAACTAACCAA
ATGGAGCAGAATGGTCAAGTGATGAATATTACTAATAGTGCTCATGAGAATAAAACAAAA
GGTGATTCTATTCAGAATGAGAAAAATCCTAACCCAATAGAATCACTGGAAGAAGAATCT
GCTTTCAAAACTAAAGCTGAACCTATAAGCAGCAGTATAAACAATATGGAACTAGAATTA
AATATCCACAATTCAAAAGCACCTAAAAAAAATAGGCTGAGGAGGAAGTCTTCTACCAGG
CATATTCATGCGCTTGAACTAGTCAGTAGAAATCTAAGCCCACCTAACTGTACTGAACTA
CAAATTGATAGTTGTTCTAGCAGTGAAGAGATAAAGAAAAAAAATTACAACCAAATGCCA
GTCAGGCACAGCAGAAACCTACAACTCATGGAAGATAAAGAATCTGCAACTGGAGCCAAG
AAGAACAAGCCAAATGAACAGACAAGTAAAAGACATGCCAGTGATACTTTCCCAGAACTG
AAGTTAACAAAGGTACCTGGTTCTTTTACTAACTGTTCAAATACTAGTGAAAAAGAATTT
GTCAATCCTAGCCTTTCAAGAGAAGAAAAAGAGAAACTAGAAACAGTTAAAGTGTCTAAT
AATGCCAAAGACCCCAAAGATCTCATCTTAAGTGGAGAAAGGGTTTTACAAACTGAAAGA
TCTGTAGAGAGTAGCAGTATTTCATTGGTACCTGGTACCGATTATGGCACTCAGGAAAGT
ATCTCATTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACGAAATAAATGTATG
AGTCAGTGTGCAGCATTTGAAAACCCCAAGGAACTAATTCATGGTTCTGAAGATACTAGA
AATGACACAGAAGGCTTTAAGTATCCATTGGGAAGTGAAGTTAACCACAGTCAGGAAACA
ATAGAAATAGAAGAAAGTGAACTTGATACTCAGTATTTGCAGAATACATTCAAGGTTTCA
AAGCGCCAGTCCTTTGCTCTGTTTTCAAATCCAGGAAATCCAGAAGAGGAATGTGCACAC
TCTAGGTCCTTAAAGAAACAAAGTCCAAAAGTTACTTCTGAATGTGAACAAAAGGAAAAT
CAAGGAAAGAAACAGTCTAATATCAAGCCTGTACAGACAGTTAATATCACTGCAGGCTTT
TCTGTGGTTTGTCAGAAAGATAAGCCAGTTGATAATGCCAAATGTAAAGGAGGCTCTAGG
TTTTGTCTATCATCTCAGTTCAGAGGCAACGAAACTGGACTCATTACTCCAAATAAACAT
GGACTGTTACAAAACCCATACCATATACCACCACTTTTTCCTGTCAAGTCATTTGTTAAA
ACTAAATGTAACAAAAACCTGCTAGAGGAAAACTCTGAGGAACATTCAGTGTCACCTGAA
AGAGCAGTGGGAAACAAGAACATTCCAAGTACAGTGAGCACAATTAGCCATAATAACAGA
GAAAATGCTTTTAAAGAAGCCAGCTCGAGCAATATTAATGAAGTAGGTTCCAGTGATGAA
AACATTCAAGCAGAACTAGGTAGAAACAGAGGGCCAAAATTGAATGCTGTGCTTAGATTA
GGGCTTTTGCAACCTGAGGTCTGTAAACAAAGTCTTCCTATAAGTAATAAGCATCCTGAA
ATAAAAAAGCAAGAAGTTCAGACTGTTAATACAGACTTCTCTCCATGTCTGATTTCAGAT
AACCTAGAACAGCCTATGAGTAGTCATGCGTCTGAGGTTTGTTCTGAGACTCCTGATGAT
CTGTTAGATGATGGTGAAATAAAGGAAGATACTAGTTTTGCTGAAAATGACATTAAGGAG
AGTTCTGCTGTTTTTAGCAAAAGCATCCAGAGAGGAGAGCTCAGCAGGAGCCCTAGCCCT
TTCACCCATACACATTTAGCTCAGGGTTACCGAAAAGAGGCCAAGAAATTAGAGTCCTCA
GAAGAGAACTTATCTAGTGAG
>Mouse
TGTGGCACAGATGCTCATGCCAGCTCATTACAGCCTGAGACCAGTTTATTGCTCATTGAA
GACAGAATGAATGCAGAAAAGGCTGAATTCTGTAATAAAAGCAAACAGCCTGGCATAGCA
GTGAGCCAGCAGAGCAGATGGGCTGCAAGTAAAGGAACATGTAACGACAGGCAGGTTCCC
AGCACTGGGGAAAAGGTAGGTCCAAACGCTGACTCCCTTAGTGATAGAGAGAAGTGGACT
CACCCGCAAAGTCTGTGCCCTGAGAATTCTGGAGCTACCACCGATGTTCCTTGGATAACA
CTAAATAGCAGCGTTCAGAAAGTTAATGAGTGGTTTTCCAGAACTGGTGAAATGTTAACT
TCTGACAGCGCATCTGCCAGGAGGCACGAGTCAAATGCTGAAGCAGCTGTTGTGTTGGAA
GTTTCAAACGAAGTGGATGGGGGTTTTAGTTCTTCAAGGAAAACAGACTTAGTAACCCCC
GACCCCCATCATACTTTAATGTGTAAAAGTGGAAGAGACTTCTCCAAACCAGTAGAGGAT
AATATCAGTGATAAAATATTTGGGAAATCCTATCAGAGAAAGGGAAGCCGCCCTCACCTG
AACCATGTGACTGAAATTATAGGCACATTTATTACAGAACCACAGATAACACAAGAGCAG
CCCTTCACAAATAAATTAAAACGTAAGAGAAGTACATCCCTTCAACCTGAGGACTTCATC
AAGAAAGCAGATTCAGCAGGTCAAAGGACTCCTGACAACATAAATCAGGGAACTGACCTA
ATGGAGCCAAATGAGCAAGCAGTGAGTACTACCAGTAACTGTCAGGAGAACAAAATAGCA
GGTAGTAATCTCCAGAAAGAGAAAAGCGCTCATCCAACTGAATCATTGAGAAAGGAACCT
GCTTCCACAGCAGGAGCCAAATCTATAAGCAACAGTGTAAGTGATTTGGAGGTAGAATTA
AACGTCCACAGTTCAAAAGCACCTAAGAAAAATAGGCTGAGGAGGAAGTCTTCTATCAGG
TGTGCTCTTCCACTTGAACCAATCAGTAGAAATCCAAGCCCACCTACTTGTGCTGAGCTT
CAAATCGATAGTTGTGGTAGCAGTGAAGAAACAAAGAAAAACCATTCCAACCAACAGCCA
GCCGGGCACCTTAGAGAGCCTCAACTCATCGAAGACACTGAACCTGCAGCGGATGCCAAG
AAGAACGAGCCAAATGAACACATAAGGAAGAGACGTGCCAGCGATGCTTTCCCAGAAGAG
AAATTAATGAACAAAGCTGGTTTATTAACTAGCTGTTCAAGTCCTAGAAAACAAGGGCCT
GTCAATCCCAGCCCTCAGAGAACAGGAACAGAGCAACTTGAAACACGCCAAATGTCTGAC
AGTGCCAAAGAACTCGGGGATCGGGTCCTAGGAGGAGAGCCCAGTGGCAAAACTGACCGA
TCTGAGGAGAGCACCAGCGTATCCTTGGTACCTGACACTGACTACGACACTCAGAACAGT
GTCTCAGTCCTGGACGCTCACACTGTCAGATATGCAAGAACAGGATCCGCTCAGTGTATG
ACTCAGTTTGTAGCAAGCGAAAACCCCAAGGAACTCGTCCATGGCTCTAACAATGCTGGG
AGTGGCACAGAGGGTCTCAAGCCCCCCTTGAGACACGCGCTTAACCTCAGTCAGGAGAAA
GTAGAAATGGAAGACAGTGAACTTGATACTCAGTATTTGCAGAATACATTTCAAGTTTCA
AAGCGTCAGTCATTTGCTTTATTTTCAAAACCTAGAAGTCCCCAAAAGGACTGTGCTCAC
TCTGTGCCCTCAAAGGAACTGAGTCCAAAGGTGACAGCTAAAGGTAAACAAAAAGAACGT
CAGGGACAGGAAGAATTTGAAATCAGTCACGTACAAGCAGTTGCGGCCACAGTGGGCTTA
CCTGTGCCCTGTCAAGAAGGTAAGCTAGCTGCTGATACAATGTGTGATAGAGGTTGTAGG
CTTTGTCCATCATCTCATTACAGAAGCGGGGAGAATGGACTCAGCGCCACAGGTAAATCA
GGAATTTCACAAAACTCACATTTTAAACAATCAGTTTCTCCCATCAGGTCATCTATAAAA
ACTGACAATAGGAAACCTCTGACAGAGGGACGATTTGAGAGACATACATCATCAACTGAG
ATGGCGGTGGGAAATGAGAACCTTCAGAGTACAGTGCACACAGTTAGCCTGAATAACAGA
GGAAATGCTTGTCAAGAAGCCGGCTCGGGCAGTATTCATGAAGTATGTTCCACTGGTGAC
TCCTTCCCAGGACAACTAGGTAGAAACAGAGGGCCTAAGGTGAACACTGTGCCTCCATTA
GATAGTATGCAGCCTGGTGTCTGTCAGCAAAGTGTTCCTGTAAGTGATAAGTATCTTGAA
ATAAAAAAGCAGGAGGGTGAGGCTGTCTGTGCAGACTTCTCTCCATGTCTATTCTCAGAC
CATCTTGAGCAATCTATGAGTGGTAAGGTTTTTCAGGTTTGCTCTGAGACACCTGATGAC
CTGCTGGATGATGTTGAAATACAGGGACATACTAGCTTTGGTGAAGGTGACATAATGGAG
AGATCTGCTGTCTTTAACGGAAGCATCCTGAGAAGGGAGTCCAGTAGGAGCCCTAGTCCT
GTAACCCATGCATCGAAGTCTCAGAGTCTCCACAGAGCGTCTAGGAAATTAGAATCGTCA
GAAGAGAGCGACTCCACTGAG