APPENDIX 1B Common File Formats

  1. Shonda A. Leonard (discussion of FASTA and GenBank file formats),
  2. Timothy G. Littlejohn (discussion of NCBI descriptor lines)1,
  3. Andreas D. Baxevanis (discussion of PHYLIP, MSF, and NEXUS file formats)2

Published Online: 1 JAN 2007

DOI: 10.1002/0471250953.bia01bs16

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Leonard, S. A., Littlejohn, T. G. and Baxevanis, A. D. 2007. Common File Formats. Current Protocols in Bioinformatics. 16:1B:A.1B.1–A.1B.9.

Author Information

  1. 1

    IBM Life Sciences, St. Leonards, NSW, Australia

  2. 2

    Bethesda, Maryland

Publication History

  1. Published Online: 1 JAN 2007
  2. Published Print: DEC 2006

This is not the most recent version of the article. View current version (21 MAR 2014)


This appendix discusses a few of the file formats frequently encountered in bioinformatics. Specifically, it reviews the rules for generating FASTA files and provides guidance for interpreting NCBI descriptor lines, commonly found in FASTA files. In addition, it reviews the construction of GenBank, Phylip, MSF and Nexus files.


  • file format;
  • FASTA;
  • NCBI descriptor lines;
  • GenBank;
  • Phylip;
  • MSF;
  • Nexus