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aligntolweb2ot

script for aligning Tree of Life Web Project backbone tree to Open Tree of Life's reference taxonomy.

avian-influenza-analyses

beastplugin

An example of external plugin for BEAST

biostatscourse

bootstrap-open-tree-software

Some utility scripts and files for helping developers get a new dev machine running with OpenTreeOfLife software builds

bull

simulator under the Halpern-Bruno (1998) model of coding sequence evolution

bullsim

DNA/AA sequence simulator that uses the Halpern and Bruno 1998 model of evolution

centroid-decomposition

decomposes a large tree into trees with overlapping subsets

chimne-ssweep

mcmc for coalescent with partial selective sweep

collections-1

Tree collections

cphyprob

C-extension of Python for calculating likelihoods in the context of phylogenetic trees

datelife

R package containing datelife's core functionality

dayhoff

thoughts on a high-level, imaginary language that would save us all a lot of time (if someone were to implement it).

dendrobites

examples of using DendroPy

dockerot

eebprogramming

routines to support a python language course for organismal biology (and associated LaTeX slides)

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

examl

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI

gb2acc-gi-taxon

Parsing Accession to taxon mapping from GenBank flat files

gene-tree-divers-sim

scripts for testing the effect of using a gene tree instead of a species tree to estimate changes in speciation rates

genomics_general

General tools for genomic analyses.

git-branch-tutorial-data

git-intro-swc-ks

Software carpentry example code for calculating a support cutoff by analyzing lots of datasets and reporting a support cutoff that is greater than 95% of them.

git-novice

Version Control with Git

graph-template-library

GTL (Graph Template Library) is a STL based library, which provides necessary classes and algorithms for the work with graphs.

grokking-git

honey_badger_fish

Python library for mapping between NeXML and NexSON formats

host-para-geo-sim

a simple simulator of host and parasite trees on a grid to mimic biogeographic patterns

intro-python-phylogenetics

a tutorial for teaching the basics of python written using an example of phylogenetics web services.

iq-tree

Efficient phylogenomic software by maximum likelihood