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¶
clustalw(1), seaview(1), t_coffee(1).AUTHORS¶
Robert Elgar- Wrote Muscle.
- Wrote this manpage.
- Updated this manpage.
COPYRIGHT¶
Copyright © 2003, 2004 Steffen Moeller (manpage)02/06/2008 | muscle 3.7 |