neherlab

allflu

krisp

visualization repository for the 2019 nextstrain workshop at KRISP

2019-krisp-nextstrain-workshop

Tutorials, data, and results of the 2019 KRISP nextstrain workshop

EV_D68_analysis

scripts that generate figures for Dyrdak et al 2018 manuscript

betatree

Generate and analyze beta coalescent trees

enterovirus_nextstrain

HIV_fitness_landscape

Analysis of fitness landscape of HIV-1 from longitudinal data

multiflu

interactive flu trees side-by-side

treetime_validation

HIV_time_of_infection

Estimating time of HIV-1 infection from next-generation sequence diversity (code and data)

HIVEVO_reservoir

Establishment and stability of the latent HIV-1 DNA reservoir

timetree_viewer

hivwholeweb

Web application for deep sequencing on longitudinal HIV-1 samples from patients.

ratchet

treetool

tool to build and visualize annotated influenza phylogenies based on blab/nextflu

nextstrain_base

pipeline components for realtime virus analysis

seqanpy

Python wrapper of some SeqAn functions

hivwholeseq

Data processing pipeline for HIV next-gen sequencing

HIVEVO_figures

pid

Manuscript: Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing

reccoal

Manuscript: Coalescence and genetic diversity in sexual populations under selection

ctlfit

Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data

synmut

Manuscript: Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution.

PoissonNMF

ImageJ plugins for blind decomposition of fluorencence microscopy data