https://github.com/linsalrob/phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
https://github.com/linsalrob/phageproteomictree
awesomeness bioinformatics evolution evolutionary-algorithms phage phylogenetic-trees phylogenetics taxonomy
Last synced: about 2 months ago
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The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
- Host: GitHub
- URL: https://github.com/linsalrob/phageproteomictree
- Owner: linsalrob
- License: mit
- Created: 2017-04-15T19:24:53.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2024-09-07T02:48:09.000Z (9 months ago)
- Last Synced: 2024-09-07T04:49:19.760Z (9 months ago)
- Topics: awesomeness, bioinformatics, evolution, evolutionary-algorithms, phage, phylogenetic-trees, phylogenetics, taxonomy
- Language: Perl
- Homepage:
- Size: 25.7 MB
- Stars: 4
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
- License: LICENSE
- Citation: CITATION.md
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README
# Phage Proteomic Tree
The phage proteomic tree is a unifying proteomic taxonomy for viruses. The problem with viruses is that there is no single gene that can be used for taxonomy, and so you have to combine distances some how.
In 1999, Edwards and Rohwer started testing different techniques for combining taxonomy of viruses, and comparing them to known literature. We had less than 50 phage genomes in the first iterations, but by the [time of publication](http://jb.asm.org/content/184/16/4529.short) in 2002 there were 105 complete phage genomes. Now there are thousands.
This code is the original code (some of it has been slightly updated to fix major bugs) to generate the phage proteomic tree.
In the directory [spounavirus](spounavirus) we walk through building a phage proteomic tree for 93 spounaviridae as part of a joint collaborative effort that [Evelien Adriaenssens](https://scholar.google.com/citations?user=58SHSIkAAAAJ&hl=en) is organising.