muscle(1) [debian man page]

MUSCLE(1)							   Muscle Manual							 MUSCLE(1)

NAME

       muscle - Multiple Protein Sequence Alignment

SYNOPSIS

       muscle -in input file (fasta) [-out output file (default fasta)] [-diags] [-log log file] [-maxiters n] [-maxhours n] [-maxmb m] [-html]
	      [-msf] [-clw] [-clwstrict] [-log[a] logfile] [-quiet] [-stable] [-group] [-version]

DESCRIPTION

       This manual page documents briefly the muscle command.

       muscle aligns protein sequences and is considered superior and faster than Clustal W.

OPTIONS

       -in input file
	   Path to FASTA formatted input file

       -out output file
	   Path to output file, FASTA formatted by default

       -diags
	   Find diagonals (faster for similar sequences)

       -maxiters n
	   Maximum number of iterations (integer, default 16)

       -maxhours n
	   Maximum time to iterate in hours (default no limit)

       -maxmb m
	   Maximum memory to allocate in Mb (default 80% of RAM)

       -html
	   Write output in HTML format (default FASTA)

       -msf
	   Write output in MSF format (default FASTA)

       -clw
	   Write output in Clustal W format (default FASTA)

       -clwstrict
	   As -clw, with 'CLUSTAL W (1.81)' header

       -log[a] logfile
	   Log to file (append if -loga, overwrite if -log)

       -quiet
	   Do not write progress messages to stderr

       -stable
	   Output sequences in input order (default is -group)

       -group
	   Group sequences by similarity (this is the default)

       -version
	   Display version information and exit

SEE ALSO

       clustalw(1), seaview(1), t_coffee(1).

AUTHORS

       Robert Elgar
	   Wrote Muscle.

       Steffen Moeller <moeller@debian.org>
	   Wrote this manpage.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Updated this manpage.

COPYRIGHT

       Copyright (C) 2003, 2004 Steffen Moeller (manpage)
       Copyright (C) 2007, 2008 Charles Plessy (manpage)

       Muscle is in the public domain, and therefore not subjected to copyright.

       This manual page was written by Steffen Moeller moeller@debian.org for the Debian(TM) system (but may be used by others). Permission is
       granted to copy, distribute and/or modify this document as if it were in public domain.

muscle 3.7							    02/06/2008								 MUSCLE(1)

PROBCONS(1)							  Probcons Manual						       PROBCONS(1)

NAME

       probcons - align multiple protein sequences and print to standard output

SYNOPSIS

       probcons [OPTION] [MFAFILE] [MFAFILE]

DESCRIPTION

       probcons is a tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and
       consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE
       benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing
       an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14%
       more correctly aligned columns than those of DIALIGN.

       probcons aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a
       single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than
       (">") symbol in the first column.

OPTIONS

       -clustalw
	   use CLUSTALW output format instead of MFA

       -c --consistency REPS
	   use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

       -ir --iterative-refinement REPS
	   use 0 <= REPS <=1000 (default: 100) passes of iterative-refinement

       -pre --pre-training REPS
	   use 0 <= REPS <= 20 (default: 0) rounds of pretraining

       -pairs
	   generate all-pairs pairwise alignments

       -viterbi
	   use Viterbi algorithm to generate all pairs (automatically enables -pairs)

       -v --verbose
	   Report progress while aligning (default: off)

       -annot FILENAME
	   write annotation for multiple alignment to FILENAME

       -t --train FILENAME
	   compute EM transition probabilities, store in FILENAME (default: no training)

       -e --emissions
	   also reestimate emission probabilities (default: off)

       -p --paramfile FILENAME
	   read parameters from FILENAME (default: )

       -a --alignment-order
	   print sequences in alignment order rather than input order (default: off)

SEE ALSO

       o   You can find more information in the manual of ProbCons, which is located in /usr/share/doc/probcons/manual.pdf in Debian systems.

       o   An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA(1), is also
	   distributed in the ProbCons Debian package.

       o    pc-makegnufile(1), pc-compare(1), pc-project(1), which are distributed separately in the probcons-extra package.

REFERENCE

       Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence
       Alignment. Genome Research 15: 330-340.

AUTHORS

       Chuong Do <chuongdo@cs.stanford.edu>
	   Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science,
	   Stanford University.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       This program and its manpage are in the public domain.

probcons 1.12							    2007-04-04							       PROBCONS(1)