Repositories list

• midtools

  Public
  Multiple Infection Detection - Python for detecting multiple infections from sequence reads and trying to pick them apart

  Python

  •11 fork•11 star•33 issues•33 pull requests•Updated Apr 14, 2026Apr 14, 2026

• dark-matter

  Public
  Virus discovery

  Python

  •

  MIT License

  •88 forks•1717 stars•3838 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• predicting_influenza_using_convergence_ms_public

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• beast2-xml

  Public
  Python code to generate BEAST2 XML files

  Python

  •

  MIT License

  •44 forks•2222 stars•66 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• bermejo_netzl_et_al2025

  Public
  This repository contains the code and data for the manuscript by Bermejo, M., Netzl, A., et al. 2025

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• ae

  Public
  acmacs-e

  C++

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• mapdeduce

  Public
  Testing amino acid polymorphisms associated with regions in antigenic space

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• acorgdb

  Public
  Python tools for interacting with antigen, sera and titration databases.

  Python

  •00 forks•33 stars•22 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• receptor-binding-sites

  Public
  Depositing information and structures related to location of receptor binding sites in various HA structures

  Promela

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 4, 2026Jan 4, 2026

• ESFLU_antigenic_cartography_training_school_2025

  Public
  This repository contains the materials for the 2025 ESFLU training school on antigenic cartography

  R

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 17, 2025Oct 17, 2025

• netzl_et_al2025

  Public
  JavaScript

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 14, 2025Oct 14, 2025

• NIAID_CEIRR_antigenic_cartography_workshop2025

  Public
  This repository contains all code for the NIAID CEIRR Training Program Antigenic Cartography Workshop July 9-10, 2025

  HTML

  •

  GNU General Public License v3.0

  •44 forks•11 star•00 issues•00 pull requests•Updated Aug 7, 2025Aug 7, 2025

• acorgdb-table-editor

  Public
  JavaScript

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 24, 2025Jul 24, 2025

• seqgen

  Public
  Python code for generating sequences in FASTA format

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•11 pull request•Updated Jan 25, 2025Jan 25, 2025

• roessler_netzl_et_al2024

  Public
  Code repository for the non-human primate antigenic cartography manuscript by Rössler, Netzl, et al. 2024

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 25, 2024Nov 25, 2024

• acmacs-build

  Public
  Makefile

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Nov 5, 2024Nov 5, 2024

• slurm-pipeline

  Public
  A Python class for scheduling SLURM jobs

  Python

  •

  MIT License

  •1010 forks•6060 stars•22 issues•00 pull requests•Updated Oct 26, 2024Oct 26, 2024

• ncbi-taxonomy-database

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

  Shell

  •

  MIT License

  •22 forks•77 stars•11 issue•00 pull requests•Updated Oct 11, 2024Oct 11, 2024

• seqdb-3

  Public
  Set of tools to build and query sequence database v3

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-virus

  Public
  Modules to handle virus and influenza related stuff, e.g. virus names, passages, reassortant information

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-map-draw

  Public
  Drawing antigenic maps

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-draw

  Public
  Drawing on an image

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-chart-2

  Public
  Accessing chart data

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-tal

  Public
  Tree et al.

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• acmacs-whocc

  Public
  Programs and scripts for WHO CCs chains

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• antigenic_cartography_introduction

  Public
  HTML

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Sep 2, 2024Sep 2, 2024

• Racmacs

  Public
  Racmacs R package for performing antigenic cartography

  JavaScript

  •

  GNU Affero General Public License v3.0

  •1111 forks•2424 stars•3636 issues•11 pull request•Updated Jun 27, 2024Jun 27, 2024

• comparison_of_sars-cov-2_antigenic_characteristics

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 9, 2024Apr 9, 2024

• roessler_netzl_et_al2023a

  Public
  This repository holds the code for the species comparison between human and hamster SARS-CoV-2 neutralisation data, published by Rössler, Netzl et al.

  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2024Mar 5, 2024

• ablandscapes

  Public
  An R package for making antibody landscapes

  R

  •

  GNU Affero General Public License v3.0

  •44 forks•33 stars•11 issue•00 pull requests•Updated Feb 28, 2024Feb 28, 2024