phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
Science Score: 54.0%
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The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
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README.md
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 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 we walk through building a phage proteomic tree for 93 spounaviridae as part of a joint collaborative effort that Evelien Adriaenssens is organising.
Owner
- Name: Rob Edwards
- Login: linsalrob
- Kind: user
- Location: Adelaide, Australia
- Company: Flinders University
- Website: http://edwards.flinders.edu.au/
- Twitter: linsalrob
- Repositories: 31
- Profile: https://github.com/linsalrob
Professor of CS and Biology Writing bioinformatics code to study viruses, phages, and metagenomes.
Citation (CITATION.md)
# Citation If you use this code, please cite: Rohwer F, Edwards R. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. [J Bacteriol 184:4529–35](http://jb.asm.org/cgi/pmidlookup?view=long&pmid=12142423)
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