muscle31
Multiple protein sequence alignment
Usage
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]
Overview
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
Releases
Unchanged in 2 releases since Debian 12 (Bookworm).