matsen

pplacer

Phylogenetic placement and downstream analysis

sbreview

Systematic biology review article on phylogenetics and the human microbiome; associated with LIRMM conference

teaching

My teaching materials.

research

My research statement.

astronaut-requests

Demo repository combining Conda, Docker, and Travis

baby-name-big-data

beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees

blackjax

BlackJAX is a sampling library designed for ease of use, speed and modularity.

compare_selection_models_2019

cowsay-test

cozy-demo

A demonstration setup showing a comfortable shell configuration

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

for-dms-viz

gohellohmsbeagle

The 'hello.cpp' example in the libhmsbeagle repository, translated to Go.

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

libsbn

Python-interface C++ library for variational Bayesian phylogenetics

OLGA

Compute generation probabilities of CDR3 amino acid and nucleotide sequences

partis

B- and T-cell receptor sequence annotation, simulation, clonal family, and germline inference

patchworklib

Patchwork for matplotlib: A subplot manager for intuitive layouts in matplotlib, seaborn, and plotnine.

PhyloInfer

Developing efficient Bayesian phylogenetic inference methods

phylopandas

Pandas DataFrames for phylogenetics

plotnine

A grammar of graphics for Python

pubtcrs

This repository contains C++ source code for TCR clustering and correlation analysis

pybind11

Seamless operability between C++11 and Python

readthedocs.org

The source code that powers readthedocs.org

SONIA

Infer selection pressures on features of amino acid CDR3 sequences.

SPURF

tfp-noodling

treeflow

wiki

SciWiki: Collective KnowledgeBase for Scientific Data and Use