This is the command muscle that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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