readseq - Reads and writes nucleic/protein sequences in various
formats
readseq [-options] in.seq > out.seq
This manual page documents briefly the readseq 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
documentation in text form, see below.
readseq reads and writes biosequences (nucleic/protein) in
various formats. Data files may have multiple sequences. readseq is
particularly useful as it automatically detects many sequence formats, and
interconverts among them.
- Formats which readseq
currently understands:
-
-
* IG/Stanford, used by Intelligenetics and others
-
* GenBank/GB, genbank flatfile format
-
* NBRF format
-
* EMBL, EMBL flatfile format
-
* GCG, single sequence format of GCG software
-
* DNAStrider, for common Mac program
-
* Fitch format, limited use
-
* Pearson/Fasta, a common format used by Fasta programs and others
-
* Zuker format, limited use. Input only.
-
* Olsen, format printed by Olsen VMS sequence editor. Input only.
-
* Phylip3.2, sequential format for Phylip programs
-
* Phylip, interleaved format for Phylip programs (v3.3, v3.4)
-
* Plain/Raw, sequence data only (no name, document, numbering)
-
+ MSF multi sequence format used by GCG software
-
+ PAUP's multiple sequence (NEXUS) format
-
+ PIR/CODATA format used by PIR
-
+ ASN.1 format used by NCBI
-
+ Pretty print with various options for nice looking output. Output
only.
-
+ LinAll format, limited use (LinAll and ConStruct programs)
-
+ Vienna format used by ViennaRNA programs
-
- See the included
"Formats" file for detail on file formats.
-
The programs are documented fully in text form. See the files in
/usr/share/doc/readseq
This manual page was written by Stephane Bortzmeyer
<bortzmeyer@debian.org>, for the Debian GNU/Linux system (but may be
used by others).