Running ClustalW
ClustalW (v.1.82) is on Beagle.
If your sequences are in a file ("myfile") in one of these formats - NBRF/PIR, EMBL/UniProt, Fasta, GDE, ALN/ClustalW,
GCG/MSF, RSF - an alignment can be performed with the following command:
beagle>clustalw myfileTwo files are created, myfile.aln file holding the alignment, and myfile.dnd file which describes the guide tree.
More options are revealed if only the program name is entered:
beagle> clustalwEntering "H" will walk you through the possible options and explain many of the alterable params.
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******** CLUSTAL W (1.82) Multiple Sequence Alignments ********
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1. Sequence Input From Disc
2. Multiple Alignments
3. Profile / Structure Alignments
4. Phylogenetic trees
S. Execute a system command
H. HELP
X. EXIT (leave program)
Your choice: