MacFormat 1996 March

home *** CD-ROM | disk | FTP | other *** search

/ MacFormat 1996 March / macformat-035.iso / Shareware City / Science / DNA stacks 1.1 / Sample Input⁄Output / 12S rRNA / Samples to input / Phylip Outfile (example input) < prev

Wrap

Text File | 1990-11-15 | 13.2 KB | 267 lines | [TEXT/MSWD]

----------------------------------------------------------------------- Sample Output:Phylip Output, Thursday, November 15, 1990 5:41 PM DNA parsimony algorithm, version 3.31 5 species, 448 sites Name Sequences ---- --------- vertcow AGGGTGACGG GCGGTGTGTG CGTGCTTCAT GGCCTAATTC AA-CTAAGCA CTCTATTCTT verthum .......... .........A ..C......G ....CTG... .......... .....C.... vertmus .......... .......... ...A...... T..TC..... ..T-.....T .......... vertxen .......... .......... ..C...C..G ....GTT..A ..GAGG.A.T ....TG.T.C zurchin ..A....... ...A.....A ..CAT.C..G A..TCTT... .G..CCCATT T......TGG vertcow AGTTTACTGC TAAATCCTCC TTTGGTT--A TTGGTTTCAT AA-TAACTTT CGTGCTTGAT verthum .......... .......A.. ..C.ACCC.T .AA....... ...GGG..A. ...--A-.T. vertmus .A......A. .......... ..A.TCC..T ..A....... ..AGGG-.A. A..--AATG. vertxen TC........ .......G.. ...TC.CGAT C......... .GAG.T.... ...--.-T.. zurchin G.C....... .G.....AA. ..CTAAAGA. ...-...... TTC..T-... ..C--.-.G. vertcow TCTCTTGGTG TAGAGAATGT AGCCCATTTC TTCCCATTTC ATAGGTTACA CCTTGACCTA verthum .-...G..-. ....A..... .......... ..G...CC.. ..G..C.... .......... vertmus ...T..AT-A A-..A..... .......... .......... ..T..C.... .......... vertxen ...AAG.T-A ....A..... .......... ......C... ...T.C.... .........G zurchin CG.----T-A A.A.C.T... ...T..C.CA ......GC.T ..GT.C.G.. ......T..G vertcow ACGTTTTTAT GTATCATAAT TA--CGCTTA CTTTTTTTCC TTTTT-AGGG TTTGCTGAAG verthum ....C....C ..GGGTACT. G-........ ....G.AG.. ..CA.C.... .......... vertmus .......... ..T.G..TC. .TTG.--... ....-AA.A. C....T.... .......... vertxen ....G..G.. .A.AA..C.. ....A..C.. ..AAGAA..T C.CACG...- .GG....GC. zurchin ....C.GG-- .A..TT.CCC ..GGA..CA. ...------T C..AAG.A.- .AGA..T.C. vertcow ATGGCGGTAT ATAGACTGTA TTAGCAAGAA TTGGTGAGGT TTATCGGGGT TTATCGATTA verthum .......... ....G...A- ---......G G......... .G........ .......... vertmus .......... ....G...A. .........G A......... AG.G...... .......... vertxen .C..T..... ....G.G.GT ..G....... G......... ...G..A..G G......... zurchin .C.AT..... .C.AG...AT ...-...A.G .......... G.T...T..A .........C vertcow TAGAACAGGC TCCTCTAGAA GGATATAAAG CACCGCCAAG TCCTTTGAGT TTTAAGCTGT verthum C......... .........G ......G... ........G. .......... .......... vertmus .......... .........T .......... T......... .......... ........A. vertxen C......... ........GT ..G.T.GG.. .......... .......G.. ........TA zurchin A.TGG..A.. ..-..C..GG A.G...GG.A A......... .......... .....A..T. vertcow T-GCTAGTAG TACTCTGGCG AATAATTTTG TTTATGTAA- TTATCTGTGT TTAGGGCTAA verthum G....C.... .GT....... .GC.G..... ..G.-T.T.A C.G.TGAG.. .......... vertmus G......... .T.......A ....G..... ..A.AT.T.A ....T.AG.. ...T...... vertxen G....C.... .--....... ----GA...- ..GC-....G .AG..AAA.. ...T.....G zurchin .A.T.T.... .--...CTG. ---------- -.GC-T..GG ..G.------ ...C.T.... vertcow GCATAGTGGG GTATCTAATC CCAGTTTG verthum .......... .......... ........ vertmus .......... .......... ........ vertxen .......... .......... ........ zurchin .T.....A.. .......... .TG....A Adding species: vertcow verthum vertmus vertxen zurchin Doing global rearrangements !---------! ......... One most parsimonious tree found: vertmus ! ! zurchin ! ! ! 4--vertxen ! ! 2--3-----verthum ! 1-----------vertcow remember: this is an unrooted tree! requires a total of 345.000 steps in each site: 0 1 2 3 4 5 6 7 8 9 *----------------------------------------- 0! 0 0 1 0 0 0 0 0 0 10! 0 0 0 0 1 0 0 0 0 0 20! 2 0 0 1 2 1 0 1 0 0 30! 1 2 0 0 2 2 1 2 0 0 40! 1 0 1 2 2 2 2 1 1 1 50! 2 1 0 0 0 1 2 0 1 1 60! 2 2 2 1 0 0 0 0 0 1 70! 0 0 1 0 0 0 0 0 2 1 80! 0 0 0 3 1 3 3 2 2 1 90! 2 1 1 2 1 0 0 0 0 0 100! 0 1 2 3 2 2 2 2 0 2 110! 0 1 0 1 1 1 2 2 2 3 120! 0 1 2 0 3 2 2 2 2 1 130! 2 2 1 1 0 2 0 1 0 0 140! 0 0 0 0 1 0 0 1 0 1 150! 1 0 0 1 0 0 0 2 2 0 160! 1 0 0 3 1 0 1 0 1 0 170! 0 0 0 0 0 0 0 1 0 0 180! 1 0 0 0 0 2 0 1 1 1 190! 2 0 1 2 2 3 2 1 2 3 200! 1 1 2 2 2 1 1 1 1 1 210! 0 0 0 1 2 3 3 2 2 2 220! 1 2 0 2 1 2 3 0 1 0 230! 1 0 2 1 1 0 0 1 1 1 240! 0 0 1 0 1 1 0 0 0 0 250! 0 0 1 0 1 1 0 1 0 2 260! 2 1 1 2 1 0 0 0 1 0 270! 2 3 0 0 0 0 0 0 0 0 280! 0 2 2 1 2 0 0 2 0 0 290! 2 1 0 0 0 0 0 0 0 0 300! 1 2 0 1 1 1 0 0 1 0 310! 0 0 0 1 0 0 1 0 0 1 320! 3 1 0 1 0 1 0 1 1 0 330! 1 2 0 0 0 0 0 0 0 1 340! 0 0 0 0 0 0 0 0 1 0 350! 0 0 0 0 0 0 1 0 0 2 360! 1 2 1 0 1 0 2 0 0 0 370! 0 0 3 2 0 0 0 1 1 1 380! 1 1 2 2 1 2 2 1 1 1 390! 1 1 0 2 1 2 2 0 2 1 400! 2 1 1 1 0 3 3 2 3 1 410! 1 0 0 0 3 0 1 0 0 0 420! 1 0 1 0 0 0 0 0 1 0 430! 0 0 0 0 0 0 0 0 0 0 440! 0 0 1 1 0 0 0 0 1 From To Any Steps? State at upper node ( . means same as in the node below it on tree) 1 AGGGTGACGG GCGGTGTGTG CGTGCTTCAT GGCCYAATTC 1 2 maybe .......... .......... .......... ....C..... 2 vertmus yes .......... .......... ...A...... T..T...... 2 3 yes .......... .........R ..C......G .....TD... 3 4 yes .......... .......... ......C... ......T... 4 zurchin yes ..A....... ...A.....A ...AT..... A..T...... 4 vertxen yes .......... .........G .......... ....G....A 3 verthum maybe .......... .........A .......... ......G... 1 vertcow maybe .......... .......... .......... ....T..... 1 AA-CTAAGCW CTCTATTCTT AGTTTACTGC TAAATCCTCC 1 2 no .......... .......... .......... .......... 2 vertmus yes ..T-.....T .......... .A......A. .......... 2 3 yes .......... .......... .......... .......A.. 3 4 yes ....BV.A.T .......T.B D......... .......... 4 zurchin yes .G..CCC.T. T.......GG G.C....... .G......A. 4 vertxen yes ..GAGG.... ....TG...C TC........ .......G.. 3 verthum yes .........A .....C.... .......... .......... 1 vertcow maybe .........A .......... .......... .......... 1 TTHGDYY--W TTRGTTTCAT AA?KRRCTWT CGT??W?GRT 1 2 maybe ......C..T .......... ...G.G.... ...--..... 2 vertmus yes ..A.TC.... ..A....... ..A.G.-.A. A....AATG. 2 3 maybe ..Y.A..?.. .......... .......... ......-... 3 4 yes ...T.H.GA. ..G....... .D?.AT..T. .....T.... 4 zurchin yes ..C..AA..A ...-...... TTCT..-... ..C.....G. 4 vertxen yes ..T.CT.... C......... .GA....... .......TA. 3 verthum yes ..C..C.C.. .AA....... ..-.G...A. .....A..T. 1 vertcow maybe ..T.GTT..A ..G....... ..-TAA..T. ...GCTT.A. 1 TCTCTTGK?R TAGARAATGT AGCCCATTTC TTCCCATTTC 1 2 maybe ........-. ....A..... .......... .......... 2 vertmus yes ...T..AT.A A-........ .......... .......... 2 3 yes .....G.... .......... .......... ......CY.. 3 4 maybe ...??..T.A .......... .......... .......... 4 zurchin yes CG.----... A.A.C.T... ...T..C.CA ......GC.T 4 vertxen maybe ...AA..... .......... .......... .......T.. 3 verthum yes .-.....G.G .......... .......... ..G....C.. 1 vertcow maybe .......GTG ....G..... .......... .......... 1 ATDGGYTACA CCTTGACCTA ACGTTTTTAT GTATSATHMT 1 2 maybe .....C.... .......... .......... ....G..... 2 vertmus yes ..T....... .......... .......... ..T....TC. 2 3 yes ..R....... .......... ....C..... .....W.C.. 3 4 yes ...T...... .........G .......G.. .A..D..... 4 zurchin yes ..G....G.. ......T... ......G.-- ....TT..CC 4 vertxen yes ..A....... .......... ....G..... ...AAA..A. 3 verthum yes ..G....... .......... .........C ..GG.TA.T. 1 vertcow maybe ..A..T.... .......... .......... ....C..AA. 1 TA--CGCTTA CTTT?WWTCC YTTTT?AGGG TTTGCTGAAG 1 2 maybe .......... ......A... .......... .......... 2 vertmus yes .TTG.--... ....-A..A. C....T.... .......... 2 3 yes .......... ....?..... ..YA...... .......... 3 4 yes ....A..C.. ...?.?...T C...HG...- .DG.....C. 4 zurchin yes ..GG....A. ...------. ..T.A..A.. .A.A..T... 4 vertxen yes .......... ..AAGA.... ..C.C..... .G.....G.. 3 verthum yes G-........ ....GT.G.. T.C..C.... .......... 1 vertcow maybe .......... ....TTT... T....-.... .......... 1 ATGGCGGTAT ATAGRCTGWA TTAGCAAGAR DTGGTGAGGT 1 2 maybe .......... ....G...A. .........G .......... 2 vertmus maybe .......... .......... .......... A......... 2 3 maybe .......... .........? .......... K......... 3 4 yes .C..T..... .........T .......... .......... 4 zurchin yes ...A...... .C.A...... ...-...A.. T......... 4 vertxen yes .......... ......G.G. ..G......A G......... 3 verthum yes .......... .........- ---....... G......... 1 vertcow maybe .......... ....A...T. .........A T......... 1 TKATCGGGGT TTATCGATTA TAGAACAGGC TCCTCTAGAD 1 2 no .......... .......... .......... .......... 2 vertmus yes AG.G...... .......... .......... .........T 2 3 yes .......... .......... C......... .........K 3 4 yes .T....D..D .......... .......... ........G. 4 zurchin yes G.T...T..A .........C A.TGG..A.. ..-..C...G 4 vertxen yes ...G..A..G G......... .......... .........T 3 verthum maybe .G........ .......... .......... .........G 1 vertcow maybe .T........ .......... .......... .........A 1 GGATATAAAG CACCGCCAAG TCCTTTGAGT TTTAAGCTGT 1 2 no .......... .......... .......... .......... 2 vertmus yes .......... T......... .......... ........A. 2 3 yes ......G... .......... .......... .......... 3 4 yes ..G....G.. .......... .......... ........T. 4 zurchin yes A........A A......... .......... .....A.... 4 vertxen yes ....T..... .......... .......G.. .........A 3 verthum yes .......... ........G. .......... .......... 1 vertcow no .......... .......... .......... .......... 1 K-GCTAGTAG T?CTCTGGCG AATARTTTTG TTDATKTWA? 1 2 maybe G......... .......... ....G..... ....?T...A 2 vertmus yes .......... .T.......A .......... ..A.A..T.. 2 3 yes .....C.... ..?....... .??....... ..G.-..... 3 4 yes .......... .--....... ----.?...- ...C...A.G 4 zurchin yes TA.T.T.... ......CTG. ....-----. -.......G. 4 vertxen yes .......... .......... .....A.... .....G.... 3 verthum maybe .......... .GT....... .GC....... .......T.. 1 vertcow maybe T......... .A........ ....A..... ..T..G.A.- 1 TTATYTRKGT TTAKGGCTAA GCATAGTGGG GTATCTAATC 1 2 maybe ......AG.. .......... .......... .......... 2 vertmus maybe ....T..... ...T...... .......... .......... 2 3 yes ..G..?.... .......... .......... .......... 3 4 maybe ....?..?.. ...B...... .......... .......... 4 zurchin yes ....------ ...C.T.... .T.....A.. .......... 4 vertxen yes .A..CA.A.. ...T.....G .......... .......... 3 verthum yes C...TG.... ...G...... .......... .......... 1 vertcow maybe ....C.GT.. ...G...... .......... .......... 1 CCAGTTTG 1 2 no ........ 2 vertmus no ........ 2 3 no ........ 3 4 no ........ 4 zurchin yes .TG....A 4 vertxen no ........ 3 verthum no ........ 1 vertcow no ........ Duration: 15.72 seconds.