Matsen Group

gctree

GCtree: phylogenetic inference of genotype-collapsed trees

sumrep

Summary statistics for repertoires

olmsted

B-cell repertoire and clonal family tree explorer

phippery

phip-flow

A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets

linearham

A Bayesian Phylo-HMM for B cell receptor sequence analysis

bcr-phylo-benchmark

gp-benchmark-1

larch

Inference and manipulation of history DAGs

tex-template

antigen

Simulating virus evolution and epidemiology

multidms

Joint modeling of multiple deep mutational scanning experiments

phylostability

SARS-CoV-2_spike_multidms

Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2

gp-benchmark-1-environment

Code to explore to what extent GP composite likelihoods and their derivatives correspond to more well-understood quantities

CYP-multidms

a repository for the analysis of C9 and C19 dms data

dmsa-pred

A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.

dnsm-json-database

hdag-benchmark

historydag

infection-timing

lassa-dmsa

Nextstrain build for Lassa virus

LASV-manuscript-nextstrain-dmsa

This repository holds the build code for generating a nextstrain tree with escape score predictions.

LK-SARS-CoV-2

Repository for Linda Kizazi SARS-CoV-2 manuscript Analysis

SARS-CoV-2-S2-Abs

Repository for Antibody Responses to SARS-CoV-2 S2 manuscript

sdag-nni-experiments

seasonal-flu-dmsa

Fork of seasonal-flu nextstrain build to include phenotype predictions informed by dms data.

usher

Ultrafast Sample Placement on Existing Trees

usher-clade-reconstructions

zika-dmsa

Nextstrain build for Zika virus with dms model phenotype predictions