MUSCLE(1) | Muscle Manual | MUSCLE(1) |
NAME¶
muscle - Multiple Protein Sequence AlignmentSYNOPSIS¶
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 filePath 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¶
AUTHORS¶
Robert Elgar- Wrote Muscle.
- Wrote this manpage.
- Updated this manpage.
COPYRIGHT¶
Copyright © 2003, 2004 Steffen Moeller (manpage)02/06/2008 | muscle 3.7 |