man clustalw (Commandes) - a multiple sequence alignment program
NAME
clustalw - a multiple sequence alignment program
SYNOPSIS
clustalw [options]
DESCRIPTION
This manual page documents briefly the clustalw command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has other documentation; see below.
clustalw is a program which performs simultaneous alignment of many nucleotide or amino acid sequences. It is typically run interactively, providing a menu and an online help. If you prefer to use it in command-line (batch) mode, you will have to give several options, the minimum being -infile.
OPTIONS
A summary of options are included below. For a complete description, see the last section.
- -infile=string
- Tells ClustalW to get input from the named file. Several formats are automatically recognized.
- -outfile=string
- Tells ClustalW to write output in the named file.
- -tree
- Calculates NJ tree.
- -profile
- Merges two alignments by profile alignment.
- -output=string
- Sets the output format. It can be GCG, GDE, PHYLIP or PIR.
- -quicktree
- Uses FAST algorithm for the alignment guide tree.
- -help
- Prints a short help. Warning: the syntax of the options is the VMS one. For Unix, change the / to a - and type the option name in lower case.
SEE ALSO
The -help option is a good summary. Files in /usr/share/doc/clustalw contains a lot of details. The Web page <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/> is also helpful.
AUTHOR
This manual page was written by Stephane Bortzmeyer <bortzmeyer@debian.org>, for the Debian GNU/Linux system (but may be used by others).