man poa (1): 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.

COPYRIGHTS

Copyright (C) 2001, 2006 Christopher Lee <[email protected]>. 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 <[email protected]> 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.