NAME

       poa - align a set of sequences or alignments.

SYNOPSIS

       poa [OPTIONS] [MATRIXFILE]

       One of the -read_fasta, -read_msa, or -read_msa_list arguments must be used, since a
       sequence or alignment file is required.

DESCRIPTION

       POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in
       bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior
       ability to handle branching / indels in the alignment. Partial order alignment is an
       approach to MSA, which can be combined with existing methods such as progressive
       alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly
       to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is
       10 to 30 times faster than CLUSTALW.

EXAMPLES

       poa -read_fasta multidom.seq -clustal m.aln blosum80.mat

       On Debian systems, poa can be tested using the following command:

       poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v
       /usr/share/poa/blosum80.mat

OPTIONS

   INPUT
       -read_fasta FILE
           Read in FASTA sequence file.

       -read_msa FILE
           Read in MSA alignment file.

       -read_msa2 FILE
           Read in second MSA file.

       -subset FILE
           Filter MSA to include list of seqs in file.

       -subset2 FILE
           Filter second MSA to include list of seqs in file.

       -remove FILE
           Filter MSA to include list of seqs in file.

       -remove2 FILE
           Filter second MSA to include list of seqs in file.

       -read_msa_list FILE
           Read an MSA from each filename listed in file.

       -tolower
           Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files).

       -toupper
           Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files).

   ALIGNMENT
       -do_global
           Do global alignment.

       -do_progressive
           Perform progressive alignment using a guide tree built by neighbor joining from a set
           of sequence-sequence similarity scores.

       -read_pairscores FILE
           Read tab-delimited file of similarity scores (If not provided, scores are constructed
           using pairwise sequence alignment.)

       -fuse_all
           Fuse identical letters on align rings.

   ANALYSIS
       -hb
           Perform heaviest bundling to generate consensi.

       -hbmin VALUE
           Include in heaviest bundle sequences with percent ID (as a fraction) >= VALUE.

   OUTPUT
       -pir FILE
           Write out MSA in PIR format.

       -clustal FILE
           Write out MSA in CLUSTAL format.

       -po FILE
           Write out MSA in PO format.

       -preserve_seqorder
           Write out MSA with sequences in their input order.

       -printmatrix LETTERS
           Print score matrix to stdout.

       -best
           Restrict MSA output to heaviest bundles (PIR only).

       -v
           Run in verbose mode (e.g. output gap penalties).

REFERENCE

       Please cite Grasso C, Lee C. (2004) Combining partial order alignment and progressive
       multiple sequence alignment increases alignment speed and scalability to very large
       alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12.

SEE ALSO

       The homepage of POA is http://www.bioinformatics.ucla.edu/poa

COPYRIGHTS

       Copyright (C) 2001, 2006 Christopher Lee <leec@mbi.ucla.edu>. POA is free software. You
       can redistribute it and/or modify it under the terms of the GNU General Public License as
       published by the Free Software Foundation.

       This manual page was written by Charles Plessy <charles-debian-nospam@plessy.org> for the
       Debian(TM) system (but may be used by others). Permission is granted to copy, distribute
       and/or modify this document under the terms of the GNU General Public License, Version 2
       any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in
       /usr/share/common-licenses/GPL.

COPYRIGHT

       Copyright © 2006 Charles Plessy

                                        september 26, 2006                                 POA(1)