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Mark T. Holder

Login: mtholder

Company: null

Location: null

Bio: null

Blog: http://phylo.bio.ku.edu/mark-holder

Member of

Repositories

alignToLWeb2OT: script for aligning Tree of Life Web Project backbone tree to Open Tree of Life's reference taxonomy.
beastPlugin: An example of external plugin for BEAST
biostatscourse: null
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
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: null
eebprogramming: routines to support a python language course for organismal biology (and associated LaTeX slides)
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
git-branch-tutorial-data: null
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.
graph-template-library: GTL (Graph Template Library) is a STL based library, which provides necessary classes and algorithms for the work with graphs.
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.
itsalltext: It's All Text! - Edit textareas in your browser with your favorite editor!
jds: simple server for posting file (currently dot) to be rendered in js
like-bayes-bio-4-day-workshop: null
likelihood-course-notes: likelihood-course-notes
llpllpp: C++14 wrapper around a low-level version of the phylogenetic likelihood library
maximum-weighted-bipartite-matching: C++ program to compute the maximum weighted bipartite matching of a graph
mephytis: javascript for phylogenetics using d3
mini_amendments: Test data for taxonomic amendments API (peyotl)
mini_collections: Tiny test repo for peyotl
mini_phyl: Mini repo for peyotl testing
mini_system: Alternate repo for testing peyotl
morpho-pll: unstable, untested tweaks to the PLL. Use the real PLL, not this copy!
mtholder.github.io: github pages test
mtree: morpho models on trees
ncl: Nexus Class Library
newick_utils: shell tools for processing phylogenetic trees
nexml: NeXML is an exchange standard for representing phyloinformatic data.
nodes-ed: javascript tools for phylogenetic UI
odd-OT-s: misc Open Tree scripts that don't belong in the dev repos.
old-phylesystem: The Open Tree Of Life NexSON Datastore
opentree-taxomachine: taxonomy graphdb
otcetera: C++14 lib for parsing of trees from newick, nexson, and taxonomy.tsv formats; tree calculations and manipulations
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.
OTifacts: data repo of links to resources that the Open Tree of Life produced, uses, or in the might-be-used-in-the-future category
ot-vagrant: vagrant files for configuring a virtualbox with the opentree software.
pdf2pdf: does the magical pdf-to-pdf conversion popular in academic journal submission sites
pdfminer: Python PDF Parser
peyotl: python library for interacting with Open Tree of Life resources
phlawd: phylogenetics with databases
phylesystem-0: Yet another testing repository. This one is full size for performance testing. But still temporary.
phylesystem-1: doc store for the Open Tree of Life study curation API
phylesystem_test: Testing repo which is a small subset of phylesystem
PhylogeneticMethodsCourse: LaTeX source for the notes and slides used in my phylogenetic methods course
phyloplumber: A tool for managing complex phylogenetic analysis pipelines
PhyPatClassProb: dynamic programming algorithm for calculating the probability of classes of data patterns on a phylogeny
pllpy: Python wrapper for the phylogenetic likelihood library (PLL), from the Exelixis lab. Of RAxML fame.
pomo-like-model: notes on a impl of a PoMo style model for large phylogenetic datasets
propinquity: make-based supertree pipeline - will be abandoned or moved to the Open Tree of Life repo soon
pyraphyletic: implementation of phylesystem-api built on pyramid
py-subprocess-demo: code associated with a lecture about running other processes from python.
pytbeaglehon: python wrapper around beagle-lib library for calculation of likelihoods on phylogenetic trees
rbg: python generator of rev language used by rev-bayes software for Bayesian phylogenetics (rb, for short)
revbayes_tutorials: Collection of tutorials for RevBayes
reveal: The HTML Presentation Framework
shell-novice: Software Carpentry introduction to the shell for novices.
shiba: Simulated historical island biogeography analysis
some-simple-r-examples: Some R examples for intro lectures.
standard-RAxML: null
supertree-study: scripts and texts associated with a study of the performance of large scale supertree methods
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.
tag-check: null
taxalotl: experiments in taxonomy merging
testing: Repo for testing Github API write access
tolweb2ott: code for aligning the Tree of Life Web project's hierarchy to the Open Tree of Life's Taxonomy (ott)
treeTestingDemo: Scripts for the interactive testing content associated with the slides used in the presentation at https://github.com/mtholder/TreeTopoTestingTalks
TreeTopoTestingTalks: scripts, figures, bibliography data, and notes for giving talks about confidence limits and tests on phylogenetic trees
trilodata: null
trilogenetics-website: the content for http://phylo.bio.ku.edu/fossil web page that is easier to manage through git rather than wordpress
urllib2_file: Extend urllib2 to support HTTP POST file upload
xml2json-badgerfish: python code for translating between xml and JSON

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This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.