Provided by: muscle_3.8.31-1_amd64
muscle - Multiple Protein Sequence Alignment
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]
This manual page documents briefly the muscle command. muscle aligns protein sequences and is considered superior and faster than Clustal W.
-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
Robert Elgar Wrote Muscle. Steffen Moeller <firstname.lastname@example.org> Wrote this manpage. Charles Plessy <email@example.com> Updated this manpage.
Copyright © 2003, 2004 Steffen Moeller (manpage) Copyright © 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 firstname.lastname@example.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.