Software
The lab is involved is several software development projects:
- GARLI (Zwickl)
- SATé (Kevin Liu, Tandy Warnow's group, and Randy Linder at the University of Texas; public version by Yu and Holder). See the README.txt file.
- DendroPy (Sukumaran and Holder) -- a Python library for phylogenetic scripting and pipelining, with support for reading/writing, simulation, processing, manipulation, and statistics of phylogenetic trees and characters in various formats.
- Phycas (written by Paul Lewis at U. Conn., Dave Swofford at Duke/NESCent, and Holder)
- Nexus Class Library (NCL; written by Paul Lewis at U. Conn and Holder). Documentation of the newer API changes is posted at http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/index.html. The project homepage is at http://ncl.sourceforge.net/index.html
- Ginkgo (Sukumaran and Holder) -- forward-time spatially-explicit agent-based simulation of multi-gene diploid genealogies under dynamic selection regimes for use in phylogeographic studies or method assessment.
- cPhyProb C-extension of Python for calculating likelihoods in the context of phylogenetic trees
- Also see the phylogenetic web services hosted here
- Source code and dependencies for the soon-to-be-submitted algorithm for calculating the probability of classes of data patterns are at http://phylo.bio.ku.edu/software/pattern_class_prob_and_deps.tar.gz