AB Delete Invariant Sites

--delete_invariant_sites, -dinv

Implemented in version 1.3

Description

Remove any columns where all of the residues are the same.

Arguments

'ambig' ( exact string )

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.

Examples

Input file: Mle-Panx_align.phy

 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

Usage example 1

$: alb Mle-Panx_align.phy -dinv

Output

 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

Usage example 2

Keep ambiguous residues even if they would otherwise match the other residues in the column

$: alb Mle-Panx_align.phy -dinv ambig

Output

 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