Clustalw 1.82 format conversion Des Higgins format alignment:multiple clustalw_convert clustalw_convert perl "clustalw -convert" 0 seqfile Alignment to convert (-infile) perl " -infile=$value" 1 7 formats are automatically recognised: NBRF/PIR, EMBL/SWISSPROT, Pearson (Fasta), Clustal (*.aln), GCG/MSF (Pileup), GCG9/RSF and GDE flat file. All non-alphabetic characters (spaces, digits, punctuation marks) are ignored except '-' which is used to indicate a GAP ('.' in GCG/MSF). FASTA and NBRF/PIR formats are recognised by having a '>' as the first character in the file. EMBL/Swiss Prot formats are recognised by the letters ID at the start of the file (the token for the entry name field). CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file. GCG/MSF format is recognised by one of the following: - the word PileUp at the start of the file. - the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT at the start of the file. - the word MSF on the first line of the line, and the characters .. at the end of this line. GCG/RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of the file. readseq_ok_alig perl 1 formats Output format (-output) perl " -output=$value" GCG 1 CLU GCG PIR GDE PHYLIP gdefile perl $formats eq "GDE" *.gde clufile perl $formats eq "CLU" *.aln readseq_ok_alig perl 1 phyfile perl $formats eq "PHYLIP" *.ph* readseq_ok_alig perl 1 gcgfile perl $formats eq "GCG" *.msf readseq_ok_alig perl 1 pirfile perl $formats eq "PIR" *.pir readseq_ok_alig perl 1