readseq

Usage: readseq [options] <in.seq> > <out.seq>

Description:

Converts protein and DNA sequence data formats.

Input:

• A DNA or protein sequence alignment in one of the supported formats.

Output:

• The converted seqeuences are written to stdout.

Options:

• -a[ll] - Select all sequences.
• -c[aselower] - Change to lower case.
• -C[ASEUPPER] - Change to lower case.
• -degap - Remove gap symbols.
• -i[tem=2,3,4] - Select item number(s) from several.
• -o[output=]out.seq - Redirect output.
• -p[ipe] - Pipe (command line, <stdin, >stdout).
• -r[everse] - Change to reverse complement.
• -v[erbose] - Verbose progress.
• -f[ormat=]# - Format number for output, or
• -f[ormat=]Name - Format name for output:

  IG/Stanford GenBank/GB NBRF EMBL GCG DNAStrider Fitch Pearson/Fasta Zuker (in-only)

  Olsen (in-only) Phylip3.2 Phylip Plain/Raw PIR/CODATA MSF ASN.1 PAUP/NEXUS Pretty (out-only)

Pretty format options:

• -wid[th]=# - Sequence line width.
• -tab=# - Left indent.
• -col[space]=# - Column space within sequences line on output.
• -gap[count] - Count gap characters in sequence numbers.
• -nameleft, -nameright[=#] - Name on left/right side [=max width].
• -nametop - Name at top/bottom.
• -numleft, -numright - Name on left/right side [=max width].
• -numtop, -numbot[=#] - Index on top/bottom.
• -match[=.] - Use match base for 2 .. n species.
• -interline[=#] - Blank line(s) between sequence blocks.

Warning messages:

• None

Bugs: None known.

Author: readseq was written by D. G. Gilbert