iGEM/UCSD evolutionary biology and bioinformatics group

hyphy

HyPhy: Hypothesis testing using Phylogenies

phylotree.js

Interactive viewer of phylogenetic trees

hyphy-analyses

HyPhy standalone analyses

hivtrace

tn93

TN93 fast distance calculator

datamonkey-js

Datamonkey - Run state-of-the-art statistical models through the comfort of your browser

hivtrace-viz

alignment.js

Javascript alignment viewer

ogv-dating

Scripts and results for estimating the dates of integrated HIV viruses using RNA samples from the same host

hyphy-vision

Visualize HyPhy results in your browser

idepi

IDentify EPItopes

datamonkey-js-server

selection-tutorial

BioExt

A few handy bioinformatics tools not already within BioPython

cawlign

hivclustering

Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)

pub-data

Publically available alignments (and trees) from published dN/dS analyses

LabSite

Website for the ACME Lab

autotune-paper

hivtrace-locales

Repository of hivtrace translations

autotune-data

This repository contains datasets utilized in the AUTO-TUNE manuscript for inferring HIV transmission clusters based on genetic distances.

biosampleMeta

Some biosample metadata scraping scripts for the ARGOS project

cve-site

Website for CVE

datamonkey-blog

dwh

Endothermy

hyphy-python

MSS-results

SARS-CoV-2-Dashboard

veg.github.io

Veg pages