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)
Check Out this Related Man Page
Bio::Tools::Run::Alignment::Kalign(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::Kalign(3pm) NAME
Bio::Tools::Run::Alignment::Kalign - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program SYNOPSIS
# Build a kalign alignment factory $factory = Bio::Tools::Run::Alignment::Kalign->new(@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # or where @seq_array is an array of Bio::Seq objects $seq_array_ref = @seq_array; $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: #There are various additional options and input formats available. #See the DESCRIPTION section that follows for additional details. DESCRIPTION
Please cite: Timo Lassmann and Erik L.L. Sonnhammer(2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298 http://msa.cgb.ki.se/downloads/kalign/current.tar.gz Helping the module find your executable You will need to enable Kalign to find the kalign program. This can be done in (at least) three ways: 1. Make sure the kalign executable is in your path (i.e. 'which kalign' returns a valid program 2. define an environmental variable KALIGNDIR which points to a directory containing the 'kalign' app: In bash export KALIGNDIR=/home/progs/kalign or In csh/tcsh setenv KALIGNDIR /home/progs/kalign 3. include a definition of an environmental variable KALIGNDIR in every script that will BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; } use Bio::Tools::Run::Alignment::Kalign; FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://redmine.open-bio.org/projects/bioperl/ AUTHOR - Albert Vilella Email idontlikespam@hotmail.com APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ program_name Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None program_dir Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args : new Title : new Usage : my $kalign = Bio::Tools::Run::Alignment::Kalign->new(); Function: Constructor Returns : Bio::Tools::Run::Alignment::Kalign Args : -outfile_name => $outname error_string Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional) version Title : version Usage : exit if $prog->version() < 2 Function: Determine the version number of the program Example : Returns : float or undef Args : none run Title : run Usage : my $output = $application->run(@seqs); Function: Generic run of an application Returns : Bio::SimpleAlign object Args : Arrayref of Bio::PrimarySeqI objects or a filename to run on align Title : align Usage : $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = @seq_array; # @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array. _run Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to kalign program Example : Returns : nothing; kalign output is written to a temporary file OR specified output file Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to kalign _setinput Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for kalign program Example : Returns : name of file containing kalign data input AND Args : Arrayref of Seqs or input file name _setparams Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for kalign program Example : Returns : parameter string to be passed to kalign during align or profile_align Args : name of calling object aformat Title : aformat Usage : my $alignmentformat = $self->aformat(); Function: Get/Set alignment format Returns : string Args : string Bio::Tools::Run::BaseWrapper methods no_param_checks Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) save_tempfiles Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) outfile_name Title : outfile_name Usage : my $outfile = $kalign->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to tempdir Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none cleanup Title : cleanup Usage : $kalign->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none io Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::Kalign(3pm)