kalign(1) [debian man page]

KALIGN(1)							Kalign User Manual							 KALIGN(1)

NAME

       kalign - performs multiple alignment of biological sequences.

SYNOPSIS

       kalign [infile.fasta] [outfile.fasta] [Options]

       kalign [-i infile.fasta] [-o outfile.fasta] [Options]

       kalign [< infile.fasta] [> outfile.fasta] [Options]

DESCRIPTION

       Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
       to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
       approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
       alignment.

OPTIONS

       -s -gpo -gapopen -gap_open x
	   Gap open penalty .

       -e -gpe -gap_ext -gapextension x
	   Gap extension penalty.

       -t -tgpe -terminal_gap_extension_penalty x
	   Terminal gap penalties.

       -m -bonus -matrix_bonus x
	   A constant added to the substitution matrix.

       -c -sort <input, tree, gaps.>
	   The order in which the sequences appear in the output alignment.

       -g -feature
	   Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?

       -same_feature_score
	   Score for aligning same features.

       -diff_feature_score
	   Penalty for aligning different features.

       -d -distance <wu, pair>
	   Distance method

       -b -tree -guide-tree <nj, upgma>
	   Guide tree method.

       -z -zcutoff
	   Parameter used in the wu-manber based distance calculation.

       -i -in -input
	   Name of the input file.

       -o -out -output
	   Name of the output file.

       -a -gap_inc
	   Increases gap penalties depending on the number of existing gaps.

       -f -format <fasta, msf, aln, clu, macsim>
	   The output format.

       -q -quiet
	   Print nothing to STDERR. Read nothing from STDIN.

REFERENCES

       o   Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
	   6:298

       o   Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
	   sequences allowing external features. Nucleic Acid Research 3:858?865.

AUTHORS

       Timo Lassmann <timolassmann@gmail.com>
	   Upstream author of Kalign.

       Charles Plessy <plessy@debian.org>
	   Wrote the manpage.

COPYRIGHT

       Copyright (C) 2004, 2005, 2006, 2007, 2008 Timo Lassmann

       Kalign 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 <plessy@debian.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 same terms as kalign itself.

       On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.

kalign 2.04							 February 25, 2009							 KALIGN(1)

POA(1)																	    POA(1)

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 (C) 2006 Charles Plessy

								september 26, 2006							    POA(1)