mtholder/mini_phyl
Mini repo for peyotl testing
Developer Profile
mtholder
Discovered public repositories for mtholder in the GitHub catalog.
mtholder/mini_system
Alternate repo for testing peyotl
mtholder/ot-dev-script-bin
This is a collection shell script that MTH uses to cut down on typing when working on open-tree coding. It is probably not of interest to others.
mtholder/phylesystem_test
Testing repo which is a small subset of phylesystem
mtholder/honey_badger_fish
Python library for mapping between NeXML and NexSON formats
mtholder/host-para-geo-sim
a simple simulator of host and parasite trees on a grid to mimic biogeographic patterns
mtholder/shiba
Simulated historical island biogeography analysis
mtholder/xml2json-badgerfish
python code for translating between xml and JSON
mtholder/some-simple-r-examples
Some R examples for intro lectures.
mtholder/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.
mtholder/swc-tree-support-ex
Software carpentry example code for calculating a support cutoff by analyzing lots of dataset and determing the cutoff greater than 95% of them.
mtholder/chimne-ssweep
mcmc for coalescent with partial selective sweep
mtholder/treeTestingDemo
Scripts for the interactive testing content associated with the slides used in the presentation at https://github.com/mtholder/TreeTopoTestingTalks
mtholder/mephytis
javascript for phylogenetics using d3
mtholder/trilogenetics-website
the content for http://phylo.bio.ku.edu/fossil web page that is easier to manage through git rather than wordpress
mtholder/ot-vagrant
vagrant files for configuring a virtualbox with the opentree software.
mtholder/tolweb2ott
code for aligning the Tree of Life Web project's hierarchy to the Open Tree of Life's Taxonomy (ott)
mtholder/supertree-study
scripts and texts associated with a study of the performance of large scale supertree methods
mtholder/standard-RAxML
Public repository.
mtholder/likelihood-course-notes
likelihood-course-notes
mtholder/itsalltext
It's All Text! - Edit textareas in your browser with your favorite editor!
mtholder/maximum-weighted-bipartite-matching
C++ program to compute the maximum weighted bipartite matching of a graph
mtholder/graph-template-library
GTL (Graph Template Library) is a STL based library, which provides necessary classes and algorithms for the work with graphs.
mtholder/ncl
Nexus Class Library
mtholder/opentree-taxomachine
taxonomy graphdb
mtholder/bootstrap-open-tree-software
Some utility scripts and files for helping developers get a new dev machine running with OpenTreeOfLife software builds
mtholder/py-subprocess-demo
code associated with a lecture about running other processes from python.
mtholder/bull
simulator under the Halpern-Bruno (1998) model of coding sequence evolution
mtholder/phlawd
phylogenetics with databases
mtholder/TreeTopoTestingTalks
scripts, figures, bibliography data, and notes for giving talks about confidence limits and tests on phylogenetic trees
mtholder/pytbeaglehon
python wrapper around beagle-lib library for calculation of likelihoods on phylogenetic trees
mtholder/PhyPatClassProb
dynamic programming algorithm for calculating the probability of classes of data patterns on a phylogeny
mtholder/nodes-ed
javascript tools for phylogenetic UI
mtholder/centroid-decomposition
decomposes a large tree into trees with overlapping subsets
mtholder/bullsim
DNA/AA sequence simulator that uses the Halpern and Bruno 1998 model of evolution
mtholder/PhylogeneticMethodsCourse
LaTeX source for the notes and slides used in my phylogenetic methods course
mtholder/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
mtholder/cPhyProb
C-extension of Python for calculating likelihoods in the context of phylogenetic trees
mtholder/phyloplumber
A tool for managing complex phylogenetic analysis pipelines
mtholder/urllib2_file
Extend urllib2 to support HTTP POST file upload
mtholder/eebprogramming
routines to support a python language course for organismal biology (and associated LaTeX slides)
mtholder/beastPlugin
An example of external plugin for BEAST