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This repository contains the code for the manuscript "Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography" by Annika Rössler, Antonia Netzl, et. al., 2023

slurm-pipeline

A Python class for scheduling SLURM jobs

Python

Racmacs

Racmacs R package for performing antigenic cartography

JavaScript

dark-matter

Virus discovery

Python

beast2-xml

Python code to generate BEAST2 XML files

Python

figtree-recolor

A script to re-color a FigTree saved Nexus file

Python

ncbi-taxonomy-database

How to make a mysql or sqlite database of NCBI taxonomy data for use with the dark-matter lineage fetcher

Shell

accourse2019

Repository for course materials for the antigenic cartography and antibody landscapes course 2019

pymds

Metric multidimensional scaling in python

Python

acmacs-build

Makefile

gor4

Python class providing an interface to GOR4 amino acid structure prediction C code

acmacs-py

Python module for acmacs

Python

simple-slurm-loop

Simple shell scripts to run a looping job on SLURM

Shell

ablandscapes

An R package for making antibody landscapes

light-matter

The lighter side of the dark side

Roff

mapping_SARS-CoV-2_antigenic_relationships_and_serological_responses

HTML

acutilsLite

cdplot

BLAST hit plotter for CD

JavaScript

py3seq

Python wrapper for the 3seq recombination detection algorithm

Python

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"

2018-cambridge-python-course

Notes and code from a May 2018 course on Python and the shell

lispmds

acmacs.r

acorg/roessler_netzl_et_al2023

acorg

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