poa - align a set of sequences or alignments.

       Copyright © 2006 Charles Plessy

                                               september 26, 2006                                         POA(1)

       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.

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.

poa-read_fastamultidom.seq-clustalm.alnblosum80.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

       poa - align a set of sequences or alignments.

INPUT-read_fastaFILE
           Read in FASTA sequence file.

       -read_msaFILE
           Read in MSA alignment file.

       -read_msa2FILE
           Read in second MSA file.

       -subsetFILE
           Filter MSA to include list of seqs in file.

       -subset2FILE
           Filter second MSA to include list of seqs in file.

       -removeFILE
           Filter MSA to include list of seqs in file.

       -remove2FILE
           Filter second MSA to include list of seqs in file.

       -read_msa_listFILE
           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_pairscoresFILE
           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.

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

   OUTPUT-pirFILE
           Write out MSA in PIR format.

       -clustalFILE
           Write out MSA in CLUSTAL format.

       -poFILE
           Write out MSA in PO format.

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

       -printmatrixLETTERS
           Print score matrix to stdout.

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

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

       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.

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

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.