Pinned Repositories
evolsim
Student evolution paper exercise
GTP
Megan Owen and Scott Provan's java implementation of their GTP algorithm for calculating the geodesic distance between phylogenetic trees
phylo_utils
Likelihood calculation utilities - pruning algorithm, phylogenetic models...
pllpy
Python wrapper for the phylogenetic likelihood library (PLL), from the Exelixis lab. Of RAxML fame.
python_tools_on_github
Some useful bioinformatics / phylogenetics python code that I've written and sometimes even use
scluster
An implementation of the self-tuning spectral clustering algorithm described in Zelnik-Manor and Perona (2004)
sigfit
Flexible Bayesian inference of mutational signatures
tree_distance
Implementation of geodesic, Robinson-Foulds and Euclidean tree distance metrics
treeCl
Clustering phylogenetic trees with python
Mixed
Repo of simple scripts used by TCG
kgori's Repositories
kgori/python_tools_on_github
Some useful bioinformatics / phylogenetics python code that I've written and sometimes even use
kgori/GTP
Megan Owen and Scott Provan's java implementation of their GTP algorithm for calculating the geodesic distance between phylogenetic trees
kgori/ensembl_project
Counting gene duplications
kgori/pybeagle
Wrapper to beagle phylogenetic likelihood calculation library
kgori/evolsim
Student evolution paper exercise
kgori/bpp
Estimate pairwise sequence distances by maximum likelihood
kgori/bpp_wrappers
kgori/clustering_project
kgori/colourmap
kgori/DarwinHighlight
Darwin Syntax Highlighting for Sublime Text / TextMate
kgori/DendroPy
A Python library for phylogenetic scripting, simulation, data processing and manipulation.
kgori/fret
Ferret data manipulation scripts and html
kgori/gapmasker
Masks gaps from simulated alignments according to a template
kgori/ggparallel
R package for creating hammock plots and parallel sets plots using the ggplot2 framework.
kgori/go_phylo
A newick lexer and parser for phylogenetics in Go
kgori/mygolang
Learning go
kgori/package_control_channel
Default channel file for Package Control. Follow the directions at:
kgori/phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
kgori/pylogeny
Python Error and FileIO conveniences
kgori/pytc
Python wrapper for TreeCollection
kgori/rplots
ggplot code
kgori/sepp
Sate-Enabled Phylogenetic Placement (SEPP)
kgori/stirling
Computing Stirling numbers of first and second kind
kgori/tree
kgori/treeCl_EM
kgori/virtualenv
Virtual Python Environment builder