HCV Database
HCV sequence database

To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.

PHYLIP (Phylogeny Inference Package) Version 3.5c

by Joseph Felsenstein

March, 1993


(c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.


The following was extracted from Joe Felsenstein's main.doc, describing how to cite PHYLIP, the package that is used at this HIV site to create the neighbor joining trees to check your sequences:

One way is like this:

Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

If the editor for whom you are writing insists that the citation must be to a printed publication, you could cite a notice for version 3.2 published in Cladistics:

Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.


Remember -- our HIV database site provides a quick screen for potential contamination problems. Be aware that serious phylogenetic analysis will require more than this simple beginning step. Joe Felsenstein's site offers many other programs and links, and is an excellent place to get started if you are new to the field of phylogenetic analysis, or to visit if you are looking for new methods. For further information, please see the University of Washington's listing of phylogenetic analysis software available on the WEB:

To the PHYLIP homepage

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Questions or comments? Contact us at hcv-info@lanl.gov