Pinned Repositories
gapml
gctree
GCtree: phylogenetic inference of genotype-collapsed trees
hyperfreq
Bayesian tool for APOBEC hypermutation analysis
olmsted
B-cell repertoire and clonal family tree explorer
phip-flow
A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
phippery
pt
Phylogenetic topographer.
relay
Bare-bones continuous integration using Docker Hub and Slack.
sumrep
Summary statistics for repertoires
vampire
🧛 Deep generative models for TCR sequences 🧛
Matsen Group's Repositories
matsengrp/hyperfreq
Bayesian tool for APOBEC hypermutation analysis
matsengrp/pt
Phylogenetic topographer.
matsengrp/smctc
Our fork of Adam M. Johansen's Sequential Monte Carlo Template Class
matsengrp/vampire-analysis-1
Data analysis using the vampire models for immune cell receptor distributions
matsengrp/tangle
Code for working with tanglegrams.
matsengrp/ig-sw
Smith-Waterman alignment for immunoglobulins
matsengrp/curvature
Ricci-Ollivier curvature of SPR and related graphs.
matsengrp/ecgtheow
Ancestral lineage reconstruction using BEAST or RevBayes
matsengrp/goliketree
Phylogenetic likelihoods in Go via BEAGLE, just to try out the language
matsengrp/joint-inf
matsengrp/libptpll
matsengrp/sumrep-ms
Manuscript describing summary statistics for repertoires
matsengrp/lcfit
A specialized surrogate function for phylogenetic likelihoods.
matsengrp/adaLASSO-phylo
Adaptive LASSO for phylogenetics
matsengrp/auspice
Web app for visualizing pathogen evolution
matsengrp/beagle-lib
general purpose library for evaluating the likelihood of sequence evolution on trees
matsengrp/bpp-phyl
Bio++ Phylogenetic Library
matsengrp/bppsuite
Bio++ Program Suite
matsengrp/dockerfiles
matsengrp/exabayes-1.3.1-lcfit
matsengrp/ighutil
Tools for working with immunoglobulin heavy chain sequences at high throughput
matsengrp/ogrdb
antibody database web site generator
matsengrp/ogrdbweb
A static website to navigate ogrdb
matsengrp/olmsted-deploy
Olmsted deploy code
matsengrp/partis
B- and T-cell receptor sequence annotation, simulation, clonal family, and germline inference
matsengrp/PyMotifFinder
matsengrp/sbn
Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks
matsengrp/strom
Repository for C++ phylogenetics tutorial
matsengrp/trusty-scipy
The scipy stack, compiled from source on Ubuntu Trusty.
matsengrp/Visualization