matsengrp Goto Github PK

adalasso-phylo

Adaptive LASSO for phylogenetics

all-the-projects

alnclst

A simple UCLUST-like clustering algorithm for pre-aligned sequences with built in recentering

antigen

Simulating virus evolution and epidemiology

auspice

Web app for visualizing pathogen evolution

bcr-phylo-benchmark

beagle-lib

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

betarat

Bayesian analysis of contingency tables as the ratio of two binomially distributed random variables

bioboxmixcr

A biobox (http://bioboxes.org/) for Mixcr (https://github.com/milaboratory/mixcr)

bioboxpartis

This repository contains the partis project (https://github.com/psathyrella/partis) packaged into a biobox (http://bioboxes.org/).

bpp-core

Bio++ Core Library

bpp-docker

bpp-phyl

Bio++ Phylogenetic Library

bpp-seq

Bio++ Sequence Library

bppsuite

Bio++ Program Suite

cft

Clonal family tree

conda-beagle

For a Docker image containing conda and the BEAGLE phylogenetic likelihood library

curvature

Ricci-Ollivier curvature of SPR and related graphs.

cyp-multidms

a repository for the analysis of C9 and C19 dms data

dagnn

A graph neural network tailored to directed acyclic graphs that outperforms conventional GNNs by leveraging the partial order as strong inductive bias besides other suitable architectural features.

dms_variants

Analyze deep mutational scanning of barcoded variants.

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

dockerfiles

ds-data

ecgtheow

Ancestral lineage reconstruction using BEAST or RevBayes

exabayes-1.3.1-lcfit

find-dnapars-trees

gapml

gb1

Curating the GB1 data from Olson et al