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AB Delete Invariant Sites
Steve Bond edited this page Jul 3, 2017
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1 revision
Remove any columns where all of the residues are the same.
Optional. By default, ambiguous characters will be treated as if they match any of the characters they represent, so a column of AAAWAAA would be deleted because 'W' can represent and 'A' or a 'T'. To force columns to be perfectly invariant, pass in the string 'ambig'. Note that gaps and 'X' are the only ambiguous characters supported for protein sequences.
4 150
Mle-Pxα9 ---atgttag aca---tact ttcaaagttt aaaggagtta ctcctt---t
Mle-Pxα7 atggwwgtgg aaattctgtt tcccataatc aacagagcca ccgctccgat
Mle-Pxα8 atggtgctgg aag---tgct cgctctcttc ccccggctag ccccct---t
Mle-Pxα6 htgttattgg aga---tatt agcgaacttc aaaggagcga cacctt---t
taaaggtata acgatagatr acgggtggga tcaactcaat cggagtttta
cannnnngtt racatcgacg atttgagtag tcagctcaac cgaactttta
caaagtgata actctgratg acgtgtggga ccagtggaac cggagcttca
cannnnnata gttctaratg acaagtggga ccagattaac cgatgttaca
tgttcgtcct gctcgttgtc atgggaacgy ctgtcactgt ccggcaatac
tgttttactt atcgctgact ytcgccatca ctatcaccat caggcagcag
tgttcatcat gacggtcctg tttggaygta tagtgactat acggtcttac
tgttcctgct gtgtgtgatt ttcggayctg tcgtgacatt cagacagtat
$: alb Mle-Panx_align.phy -dinv
4 95
Mle-Pxα9 agtacaactt aaagttaaag agttatcttt gtaaacgaat cggtggatac
Mle-Pxα7 gwggaagttc cataacaaca agccacgtcc nngtracacc tttatagtgc
Mle-Pxα8 ggcgaggccg tctctccccc gctagccctc tgaaactcgt cgttggacgt
Mle-Pxα6 tatggaatag gaactcaaag agcgaacttc nnaagttcat caatggacga
tctgagtttc gtccgctcgt gtcaggaacg yctgctgccg caatc
tccaactttt tactatcgcg actycccatc actaccacag cagcg
ggcgagctcc atcagacggc ctgttgaygt ataggtaacg tcttc
ttcatgtacc ctgcgtgtgg atttcgayct gtcggatcaa cagtt
Keep ambiguous residues even if they would otherwise match the other residues in the column
$: alb Mle-Panx_align.phy -dinv ambig
4 110
Mle-Pxα9 ---atgtaca ---acttaaa gttaaagagt tatctt---t aaggtaaacg
Mle-Pxα7 atggwwggaa ttcgttccat aacaacaagc cacgtccgac nnnnngtrac
Mle-Pxα8 atggtgcgag ---gccgtct ctcccccgct agccct---c aagtgaaact
Mle-Pxα6 htgttatgga ---ataggaa ctcaaagagc gaactt---c nnnnnaagtt
aagtrcggtg gatactctga gtttcgtccg ctcgtgtcag gaacgyctgc
acgcgtttat agtgctccaa ctttttacta tcgcgactyc ccatcactac
cgrtgcgttg gacgtggcga gctccatcag acggcctgtt gaygtatagg
cartgcaatg gacgattcat gtaccctgcg tgtggatttc gayctgtcgg
tgccgcaatc
cacagcagcg
taacgtcttc
atcaacagtt