📄 distmat.txt
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"-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messagesInput file format It reads in a normal multiple sequence alignment file. The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis. Input files for usage example File: pax.alignPileUp MSF: 603 Type: P Check: 9004 .. Name: PAX4_HUMAN oo Len: 603 Check: 6594 Weight: 11.2 Name: PAX6_HUMAN oo Len: 603 Check: 7176 Weight: 9.1 Name: PAX3_HUMAN oo Len: 603 Check: 7760 Weight: 9.5 Name: PAX7_HUMAN oo Len: 603 Check: 4677 Weight: 13.7 Name: PAX1_HUMAN oo Len: 603 Check: 9671 Weight: 8.7 Name: PAX9_HUMAN oo Len: 603 Check: 565 Weight: 12.0 Name: PAX2_HUMAN oo Len: 603 Check: 9553 Weight: 8.7 Name: PAX5_HUMAN oo Len: 603 Check: 448 Weight: 11.2 Name: PX8A_HUMAN oo Len: 603 Check: 6763 Weight: 7.5 Name: PX8D_HUMAN oo Len: 603 Check: 5797 Weight: 7.9//PAX4_HUMAN .......... .......... .........M HQDGISSMNQ LGGLFVNGRPPAX6_HUMAN .......... .......... .......... MQNSHSGVNQ LGGVFVNGRPPAX3_HUMAN MTTLAGAVPR MMRPGPGQNY PRSGFPLEVS TPLGQGRVNQ LGGVFINGRPPAX7_HUMAN MAALPGTVPR MMRPAPGQNY PRTGFPLEVS TPLGQGRVNQ LGGVFINGRPPAX1_HUMAN .......... .......... .......... MEQTYGEVNQ LGGVFVNGRPPAX9_HUMAN .......... .......... .......... MEPAFGEVNQ LGGVFVNGRPPAX2_HUMAN .......... ........MD MHCKADPFSA MHPGHGGVNQ LGGVFVNGRPPAX5_HUMAN .......... ........MD LEKNYPTPRT SRTGHGGVNQ LGGVFVNGRPPX8A_HUMAN .......... .......... .....MPHNS IRSGHGGLNQ LGGAFVNGRPPX8D_HUMAN .......... .......... .....MPHNS IRSGHGGLNQ LGGAFVNGRPPAX4_HUMAN LPLDTRQQIV RLAVSGMRPC DISRILKVSN GCVSKILGRY YRTGVLEPKGPAX6_HUMAN LPDSTRQKIV ELAHSGARPC DISRILQVSN GCVSKILGRY YETGSIRPRAPAX3_HUMAN LPNHIRHKIV EMAHHGIRPC VISRQLRVSH GCVSKILCRY QETGSIRPGAPAX7_HUMAN LPNHIRHKIV EMAHHGIRPC VISRQLRVSH GCVSKILCRY QETGSIRPGAPAX1_HUMAN LPNAIRLRIV ELAQLGIRPC DISRQLRVSH GCVSKILARY NETGSILPGAPAX9_HUMAN LPNAIRLRIV ELAQLGIRPC DISRQLRVSH GCVSKILARY NETGSILPGAPAX2_HUMAN LPDVVRQRIV ELAHQGVRPC DISRQLRVSH GCVSKILGRY YETGSIKPGVPAX5_HUMAN LPDVVRQRIV ELAHQGVRPC DISRQLRVSH GCVSKILGRY YETGSIKPGVPX8A_HUMAN LPEVVRQRIV DLAHQGVRPC DISRQLRVSH GCVSKILGRY YETGSIRPGVPX8D_HUMAN LPEVVRQRIV DLAHQGVRPC DISRQLRVSH GCVSKILGRY YETGSIRPGVPAX4_HUMAN IGGSKPR.LA TPPVVARIAQ LKGECPALFA WEIQRQLCAE GLCTQDKTPSPAX6_HUMAN IGGSKPR.VA TPEVVSKIAQ YKRECPSIFA WEIRDRLLSE GVCTNDNIPSPAX3_HUMAN IGGSKPKQVT TPDVEKKIEE YKRENPGMFS WEIRDKLLKD AVCDRNTVPSPAX7_HUMAN IGGSKPRQVA TPDVEKKIEE YKRENPGMFS WEIRDRLLKD GHCDRSTVPSPAX1_HUMAN IGGSKPR.VT TPNVVKHIRD YKQGDPGIFA WEIRDRLLAD GVCDKYNVPS [Part of this file has been deleted for brevity]PX8A_HUMAN VSSSSSTPSS LSSSAFLDLQ QVGSGVPPFN AFPHAASVYG QFTGQALLSGPX8D_HUMAN ....KSAPGS RPS....... .....MP... .FPMLPPCTG SSRARPSSQGPAX4_HUMAN .......... .......... .....ERCLS DTPPKACLKP CWDCGSFLLPPAX6_HUMAN .......... .......... .SFTMANNLP MQPPVPSQTS SYSCMLPTSPPAX3_HUMAN NGL.SPQVM. .......... GLLTNHGGVP HQPQTDYALS PLTGGLEPTTPAX7_HUMAN NGL.SPQVM. .......... SILGNPSAVP PQPQADFSIS PLHGGLDSATPAX1_HUMAN .......... .......... GAGVAVHGGE LAAAMTFKHR EGTDRKPP..PAX9_HUMAN .......... .......... ......HNCD IPASLAFKGM QAARE.....PAX2_HUMAN .......... .......... GSYPTSTLAG MVPGSEFSGN PYSHPQYTAYPAX5_HUMAN .......... .......... GSYSAPTLTG MVPGSEFSGS PYSHPQYSSYPX8A_HUMAN REMVGPTLPG YPPHIPTSGQ GSYASSAIAG MVAGSEYSGN AYGHTPYSSYPX8D_HUMAN ERWWGPRCP. .......... DTHPTSPPAD RAAMPPLPSQ AWWQEVN...PAX4_HUMAN VIAPSCVDVA WP.CLDASLA HHLIGGAGKA TPTHFS.... ..........PAX6_HUMAN SVNGRSYDTY TPPHMQTHMN SQPMGTSGTT STGLISPGVS VPVQVPGSEPPAX3_HUMAN TVSASCSQRL DHMKSLDSLP TSQSYCPPTY STTGYSMDPV TGYQYGQYGQPAX7_HUMAN SISASCSQRA DSIKPGDSLP TSQAYCPPTY STTGYSVDPV AGYQYGQYGQPAX1_HUMAN ..SSGSKAPD ALSSLH.... ....GLPIPA STS....... ..........PAX9_HUMAN ..GSHSVTAS AL........ .......... .......... ..........PAX2_HUMAN NEAWRFSNPA LLSSPYYYSA APR.SAPAAR AAAYDRH... ..........PAX5_HUMAN NDSWRFPNPG LLGSPYYYSA AARGAAPPAA ATAYDRH... ..........PX8A_HUMAN SEAWGFPNSS LLSSPYYYSS TSRPSAPPTT ATAFDHL... ..........PX8D_HUMAN ..TLAMPMAT PPTPP..... TARPGASPTP AC........ ..........PAX4_HUMAN .....HWP.. .......... .......... .......... ..........PAX6_HUMAN DMS.QYWPRL Q......... .......... .......... ..........PAX3_HUMAN S...KPWTF. .......... .......... .......... ..........PAX7_HUMAN SECLVPWASP VPIPSPTPRA SCLFMESYKV VSGWGMSISQ MEKLKSSQMEPAX1_HUMAN .......... .......... .......... .......... ..........PAX9_HUMAN .......... .......... .......... .......... ..........PAX2_HUMAN .......... .......... .......... .......... ..........PAX5_HUMAN .......... .......... .......... .......... ..........PX8A_HUMAN .......... .......... .......... .......... ..........PX8D_HUMAN .......... .......... .......... .......... ..........PAX4_HUMAN ...PAX6_HUMAN ...PAX3_HUMAN ...PAX7_HUMAN QFTPAX1_HUMAN ...PAX9_HUMAN ...PAX2_HUMAN ...PAX5_HUMAN ...PX8A_HUMAN ...PX8D_HUMAN ...Output file format The output from the program is a file containing a matrix of the calculated distances between each of the input aligned sequences. The distances are expressed in terms of the number of substitutions per 100 bases or amino acids. Output files for usage example File: pax.distmatDistance Matrix---------------Using the Kimura correction methodGap weighting is 0.000000 1 2 3 4 5 6 7 8 9 10 0.00 96.15 137.48 128.72 161.14 160.37 157.55 154.23 164.32152.68 PAX4_HUMAN 1 0.00 111.86 109.96 156.25 149.70 143.75 135.71 150.60146.87 PAX6_HUMAN 2 0.00 26.21 131.54 143.54 162.95 151.39 163.56159.78 PAX3_HUMAN 3 0.00 145.45 138.76 158.79 149.96 167.26161.82 PAX7_HUMAN 4 0.00 44.29 120.84 123.00 131.69130.22 PAX1_HUMAN 5 0.00 123.56 130.21 131.64130.17 PAX9_HUMAN 6 0.00 36.43 53.12 64.32 PAX2_HUMAN 7 0.00 60.88 73.82 PAX5_HUMAN 8 0.00 20.37 PX8A_HUMAN 9 0.00 PX8D_HUMAN 10Data files None.Notes None.References See the following for details of the methods used: 1. "Phylogenetic Inference", Swofford, Olsen, Waddell, and Hillis, in Molecular Systematics, 2nd ed., Sinauer Ass., Inc., 1996, Ch. 11. 2. F. Tajima and M. Nei, Mol. Biol. Evol. 1984, 1, 269. 3. M. Kimura, J. Mol. Evol. 1980, 16, 111. 4. K. Tamura, Mol. Biol. Evol. 1992, 9, 678. 5. L. Jin and M. Nei, Mol. Biol. Evol. 1990, 7, 82. 6. M. Kimura, The Neutral Theory of Molecular Evolution, Camb. Uni. Press, Camb., 1983.Warnings The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis.Diagnostic Error Messages None.Exit status It always exits with status 0.Known bugs None.See also Program name DescriptionAuthor(s) Tim Carver (tcarver ⌨️ 快捷键说明
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