Antigenic Cartography's repositories
beast2-xml
Python code to generate BEAST2 XML files
accourse2019
Repository for course materials for the antigenic cartography and antibody landscapes course 2019
light-matter
The lighter side of the dark side
simple-slurm-loop
Simple shell scripts to run a looping job on SLURM
parvo-2018
FASTA alignments and BEAST2 XML files for the PNAS paper "Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans"
acbot
The Top Whack Quack Shack!
acmacs-tree-maker
Scripts for making phylogenetic tree on AC cluster
acmacs-virus
Modules to handle virus and influenza related stuff, e.g. virus names, passages, reassortant information
acmacs-webserver
Lightweight webserver with websockets support to access acmacs data
beast-mcmc
Bayesian Evolutionary Analysis Sampling Trees
csd3
Common shell setup for the Cambridge CSD3 cluster
locationdb
Location db for acmacs and related packages with the scripts for accessing and updating
mouse-bwa
SLURM pipeline for running a sample against the mouse genome using bwa
omicron-neutralization-paper
antigenic cartography and antibody landscapes related code and figures for the paper Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2022-28-01
phylo-color
Add color information to nodes in a phylogenetic tree
receptor-binding-sites
Depositing information and structures related to location of receptor binding sites in various HA structures
recombination
Experiments to investigate the effect of recombination on ML trees
seqdb
Set of tools to build and query sequence database
ssm-report
Documentation and scripts for SSM and TCs report preparation
vole-bwa
SLURM pipeline for running a sample against the vole genome using bwa