phylogenetics

Building a Simple Application Using 'libsequence'

Submitted by Jeet Sukumaran on Sun, 07/04/2010 - 01:34

Note: As pointed out by Dr. Thornton, the build methods described and given below result in the program binary being statically-linked to the libsequence library.

FASTA to NEXUS

Submitted by Jeet Sukumaran on Wed, 11/12/2008 - 19:52

Here is a quick-and-dirty script to convert FASTA files to NEXUS:

SumTrees: Summarization of Split Support on Phylogenetic Trees

SumTrees is a program by myself and Mark T. Holder to summarize non-parameteric bootstrap or Bayesian posterior probability support for splits or clades on phylogenetic trees.

It is part of the DendroPy Python library for phylogenetic computing, and has its home page at:

bootscore: A Bootstrap Tree Scoring Utility

Submitted by Jeet Sukumaran on Tue, 06/03/2008 - 02:52

bootscore is a program that maps non-parametric bootstrap support for nodes/branches on topology (typically a topology resulting from a best tree search on phylogenetic data).

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Building a Simple Application Using 'libsequence'

FASTA to NEXUS

SumTrees: Summarization of Split Support on Phylogenetic Trees

bootscore: A Bootstrap Tree Scoring Utility