NEXUS file format
From Christoph's Personal Wiki
NEXUS is the file format used by many popular programs like GDA, Paup*, Mesquite, ModelTest, MrBayes, and MacClade. Nexus file names often have a .nxs or .nex extension.
Example NEXUS files
DNA
#nexus begin data; dimensions ntax=10 nchar=705; format datatype=dna interleave=yes gap=- missing=?; matrix Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA Cow CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC Carp CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT Chicken GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC Human ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT Loach CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT Mouse ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT Rat ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT Seal CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC Whale CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC Frog CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC Cow ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA Carp ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA Chicken CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA Human GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA Loach GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA Mouse ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA Rat ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA Seal ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA Whale ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA Frog ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG Cow GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT Carp ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC Chicken GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC Human ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC Loach ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA Mouse GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT Rat GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC Seal GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA Whale GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA Frog ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC Cow TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA Carp CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA Chicken CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC Human CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT Loach CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG Mouse CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA Rat CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA Seal TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA Whale TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA Frog CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC Cow GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC Carp GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC Chicken GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC Human GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC Loach GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC Mouse GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA Rat GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC Seal GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA Whale GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC Frog GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT Cow TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT Carp TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC Chicken TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT Human TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT Loach TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC Mouse TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC Rat TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT Seal TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT Whale TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC Frog TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT Cow CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA Carp CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA Chicken CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC Human CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG Loach CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA Mouse CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC Rat CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG Seal CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC Whale CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC Frog CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC Cow CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC Carp CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT Chicken CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT Human CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC Loach CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC Mouse CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT Rat CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC Seal CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC Whale CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC Frog CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT Cow CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC Carp CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT Chicken CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC Human CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT Loach CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT Mouse CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT Rat CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC Seal CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT Whale CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC Frog CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC Cow GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA Carp GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA Chicken GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA Human GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA Loach GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA Mouse GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA Rat GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA Seal GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG Whale GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA Frog GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA Cow AAATGATCTGCGTCAATATTA---------------------TAA Carp AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA Chicken GCCTGATCCTCACTA------------------CTGTCATCTTAA Human ATA---------------------GGGCCCGTATTTACCCTATAG Loach AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA Mouse AACTGATCTGCTTCAATAATT---------------------TAA Rat AACTGATCAGCTTCTATAATT---------------------TAA Seal AAATGATCTACCTCAATGCTT---------------------TAA Whale AAATGATCTGTATCAATACTA---------------------TAA Frog AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA ; end;
Amino Acid
#NEXUS Begin data; Dimensions ntax=10 nchar=234; Format datatype=protein gap=- interleave; Matrix Cow MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Carp MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQE Chicken MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLS-SNTVDAQE Human MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQE Loach MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQE Mouse MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Rat MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Seal MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Whale MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQE Frog MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQE Cow VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Carp IEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDS Chicken VELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDS Human METVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNS Loach IEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDS Mouse VETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Rat VETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Seal VETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDS Whale VETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Frog IEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDS Cow YMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Carp YMVPTQDLAPGQFRLLETDHRMVVPMESPVRVLVSAEDVLHSWAVPSLGVKMDAVPGRLN Chicken YMTPTTDLPLGHFRLLEVDHRIVIPMESPIRVIITADDVLHSWAVPALGVKTDAIPGRLN Human YMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLN Loach YMIPTQDLTPGQFRLLETDHRMVVPMESPIRILVSAEDVLHSWALPAMGVKMDAVPGRLN Mouse YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Rat YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAIPSLGLKTDAIPGRLN Seal YMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Whale YMIPTSDLKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Frog YMIPTNDLTPGQFRLLEVDNRMVVPMESPTRLLVTAEDVLHSWAVPSLGVKTDAIPGRLH Cow QTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML------- Carp QAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS Chicken QTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSL------LSS Human QTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEM-------GPVFTL Loach QTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS Mouse QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Rat QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Seal QTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML------- Whale QTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML------- Frog QTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSML-EASL-- ; End;
References
- Maddison DR, Swofford DL, and Maddison WP (1997). NEXUS: An extensible file format for systematic information. Syst. Biol. 46:590-621. (PDF)
