mafft-homologs - aligns sequences together with homologues automatically collected from SwissProt via

KazutakaKatoh <katoh_at_bioreg.kyushu-u.ac.jp.>
           Wrote Mafft.

       CharlesPlessy <charles-debian-nospam@plessy.org>
           Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.

       Copyright © 2002-2007 Kazutaka Katoh (mafft)
       Copyright © 2007 Charles Plessy (this manpage)

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mafft-homologs 2.1                                 2007-06-09                                  MAFFT-HOMOLOGS(1)

       The accuracy of an alignment of a few distantly related sequences is considerably improved when being
       aligned together with their close homologs. The reason for the improvement is probably the same as that
       for PSI-BLAST. That is, the positions of highly conserved residues, those with many gaps and other
       additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by
       adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural
       information of a pair of sequences. Mafft-homologs in a mafft server works like this:

        1.  Collect a number (50 by default) of close homologs (E=1e-10 by default) of the input sequences.

        2.  Align the input sequences and homologs all together using the L-INS-i strategy.

        3.  Remove the homologs.

       mafft-homologs - aligns sequences together with homologues automatically collected from SwissProt via
       NCBI BLAST

-an
           The number of collected sequences (default: 50).

       -en
           Threshold value (default: 1e-10).

       -oxxx
           Options for mafft (default: " --op 1.53 --ep 0.123 --maxiterate 1000 --localpair --reorder").

       -l
           Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a
           database).

       -f
           Outputs collected homologues also (default: off).

       -w
           entire sequences are subjected to BLAST search (default: well-aligned region only)

       Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in
       accuracy of multiple sequence alignment.

       MAFFT version > 5.58.

       Either of

           lynx (when remote BLAST server is used)

           BLAST and a protein sequence database (when local BLAST is used)

mafft(1)

mafft-homologs [options] input [> output]