belvu(1) [debian man page]

BELVU(1)							   User Commands							  BELVU(1)

NAME

       belvu - View multiple alignments in good-looking colours.

SYNOPSIS

       belvu [options] <multiple_alignment>|- [X options]

	      <multiple_alignment>|- = alignment file or pipe.

DESCRIPTION

       Belvu presents multiple sequence alignments in a colourful biologically interpretable manner.

OPTIONS

       -c	   Print Conservation table.

       -l <file>   Load color code file.

       -L <file>   Load Markup color code file.

       -m <file>   Read file with matching sequence segments.

       -r	   Read alignment in 'raw' format (Name sequence).

       -R	   Do not parse coordinates when reading alignment.

       -o <format> Write alignment or tree to stdout in this format and exit.

	      Valid formats: MSF, Mul(Stockholm), Selex,

	      FastaAlign, Fasta, tree.

       -n <cutoff> Make non-redundant to <cutoff> %identity at startup.

       -Q <cutoff> Remove columns more gappy than <cutoff>.

       -q <cutoff> Remove sequences more gappy than <cutoff>.

       -P     Remove partial sequences at startup.

       -C     Don't write coordinates to saved file.

       -z <char>
	      Separator char between name and coordinates in saved file.

       -a     Show alignment annotations on screen (Stockholm format only).

       -p     Output random model probabilites for HMMER.

	      (Based on all residues.)

       -S <order>
	      Sort sequences in this order.

	      a  ->  alphabetically o -> by Swissprot organism, alphabetically s -> by score n -> by Neighbor-joining tree u -> by UPGMA tree S ->
	      by similarity to first sequence i -> by identity to first sequence

       -s <file>
	      Read in file of scores.

       -T <method> Start up with tree calculated by method:

	      n -> Neighbor-joining u -> UPGMA N -> Neighbor-joining, only show tree U -> UPGMA, only show tree c -> Don't color tree by  organism
	      o -> Don't display sequence coordinates in tree s -> Use Storm & Sonnhammer distance correction r -> Use uncorrected distances

       -b <#>
	      Print out # bootstrapped trees and exit

	      (Negative value -> display bootstrap trees on screen)

       -O <label>
	      Read organism info after this label (default OS)

       -t <title>
	      Set window title.

       -g     Draw grid line (for debugging).

       -u     Start up with uncoloured alignment (faster).

       -h     Show this help.

       -v     Show version info.

	      Some X options: -acefont <font>	Main font.  -font    <font>   Menu font.

SEE ALSO

       For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html

AUTHOR

       Erik Sonnhammer <Erik.Sonnhammer@cgb.ki.se>

VERSION

       Version 2.16, compiled Aug 18 2009

belvu 2.19							    August 2009 							  BELVU(1)

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)