The lab is involved is several software development projects:
-
host-para-geo-sim
is a geographically explicit simulator of host-parasite coevolution being developed in collaboration with
Janine Caira
,
Kirsten Jensen
,
Gavin Naylor
, and
Elizabeth Jockusch
-
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
"https://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
"https://phylo.bio.ku.edu/software/pattern_class_prob_and_deps.tar.gz