[Biopython-dev] [Biopython - Bug #3360] (New) Bio.Phylo.Applications support for FastTree

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu May 31 23:29:10 EDT 2012


Issue #3360 has been reported by Eric Talevich.

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Bug #3360: Bio.Phylo.Applications support for FastTree
https://redmine.open-bio.org/issues/3360

Author: Eric Talevich
Status: New
Priority: Low
Assignee: 
Category: 
Target version: 
URL: 


FastTree is the new hotness in maximum-likelihood tree inference, and the new default/recommendation in SATe (http://phylo.bio.ku.edu/software/sate/sate.html). It also does very fast neighbor-joining trees.

Let's create a wrapper for it in Biopython. The interface is very simple and Unix-y, taking an alignment in Phylip or FASTA format as input. Interestingly, it prints the final tree to standard output, unlike RAxML and PhyML.

Homepage:
http://www.microbesonline.org/fasttree/


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