READSEQ

READSEQ reformats nucleic acid or protein sequence files into a different format. READSEQ is particularly useful as it automatically detects many sequence formats, and interconverts among them.

Formats which readseq currently understands:

  • IG/Stanford, used by Intelliigenetics 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.

Copyright 1990 by D. G. Gilbert, Biology dept., Indiana University, Bloomington, In 47405
e-mail: gilbertd@bio.indiana.edu

Installed on the Opteron Cluster.

Version 1Feb93

READSEQ users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.

Usage: 

/biomed/bin/readseq

Other READSEQ Documentation

See also: