Repositories list

• treetime

  Public
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

  phylogenetics

  Jupyter Notebook

  •

  MIT License

  •56•228•29•5•Updated Nov 30, 2024Nov 30, 2024

• SARS2-refined-fitness

  Public
  Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• PoL1-course-materials

  Public
  Notebook and script of the PoL1 course at the university of Basel

  Jupyter Notebook

  •0•1•0•0•Updated Nov 23, 2024Nov 23, 2024

• rsv_intrahost_2024

  Public
  Workflow for RSV analyses on Nextstrain.org

  Python

  •3•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• nextclade_data_workflows

  Public
  snakemakephylogeneticsnextstrain+ 2virus-evolutionnextclade

  Python

  •1•4•10•1•Updated Nov 14, 2024Nov 14, 2024

• SARS-CoV-2_variant-reports

  Public
  Informal summaries of notable SARS-CoV-2 lineages

  covid-19sars-cov-2virus-evolution+ 1sars-cov-2-variants

  12•107•0•0•Updated Nov 11, 2024Nov 11, 2024

• pangraph

  Public
  A bioinformatic toolkit to align genome assemblies into pangenome graphs

  genomebacteriagenome-assembly+ 4pangenomepangraphbioinformaticsjulia

  Julia

  •

  MIT License

  •7•90•8•3•Updated Nov 4, 2024Nov 4, 2024

• phylogeography

  Public
  Python

  •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• CCHFV

  Public
  Python

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• h5nx-Clades

  Public
  Python

  •2•0•0•0•Updated May 7, 2024May 7, 2024

• HIV-nextclade

  Public
  Python

  •0•0•0•0•Updated May 6, 2024May 6, 2024

• simple-annotator

  Public
  Python

  •0•0•0•0•Updated Feb 29, 2024Feb 29, 2024

• spike-only

  Public
  Spike-only SARS-CoV-2 Nextstrain build

  bioinformaticsphylogeneticsaugur+ 4nextstrainsars-cov-2nextstrain-ncovsars-cov-2-variants

  Python

  •

  MIT License

  •0•2•0•0•Updated Dec 13, 2023Dec 13, 2023

• BA286

  Public
  BA.2.86 project with Sigal lab

  bioinformaticssnakemakecomputational-biology+ 7phylogeneticsnextstraintreetimesars-cov-2virus-evolutiongenomic-epidemiologysars-cov-2-variants

  Python

  •

  MIT License

  •1•2•0•1•Updated Nov 8, 2023Nov 8, 2023

• pan-genome-analysis

  Public
  Processing pipeline for pan-genome visulization and exploration

  Python

  •

  GNU General Public License v3.0

  •38•134•33•3•Updated Oct 9, 2023Oct 9, 2023

• RSV_nextclade_trial

  Public
  1•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• nextclade_data

  Public
  DO NOT USE. This is for testing new stuff on https://github.com/nextstrain/nextclade_data

  Python

  •28•0•0•0•Updated Aug 28, 2023Aug 28, 2023

• ncov-simple

  Public
  Python

  •1•2•9•1•Updated Aug 24, 2023Aug 24, 2023

• flu_clades

  Public
  Python

  •0•4•0•0•Updated Aug 23, 2023Aug 23, 2023

• outlier-detection

  Public
  Python

  •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

• minimizer

  Public
  Rust implementation of a minimizer index

  Rust

  •

  MIT License

  •1•0•0•0•Updated Aug 5, 2023Aug 5, 2023

• sc2-phylo-workflow

  Public
  demonstraion workflow for SC2 phylogenetic analysis using nextclade

  Python

  •0•0•0•0•Updated Aug 1, 2023Aug 1, 2023

• ffpopsim

  Public
  FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…

  C++

  •

  GNU General Public License v3.0

  •11•12•2•1•Updated Jul 17, 2023Jul 17, 2023

• Rpi_test_tools

  Public
  Scripts to test the Rpi for the morbidostat

  Python

  •0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

• flu-ingest

  Public
  Python

  •0•1•0•0•Updated May 9, 2023May 9, 2023

• CompBio2023

  Public
  simple viral consensus assembly

  Python

  •0•1•0•0•Updated Apr 24, 2023Apr 24, 2023

• TreeKnit-web

  Public
  TypeScript

  •

  MIT License

  •0•1•0•0•Updated Apr 21, 2023Apr 21, 2023

• SC2_variant_rates

  Public
  analyze substitution rate and mutation behavior within variants.

  TeX

  •2•2•0•0•Updated Apr 12, 2023Apr 12, 2023

• pan-genome-visualization

  Public
  Visualization of the pan-genome output by panX

  JavaScript

  •

  Other

  •22•62•7•2•Updated Apr 7, 2023Apr 7, 2023

• nextclade-dataset-template

  Public
  Template to create a simple Nextclade dataset from scratch

  Python

  •

  MIT License

  •0•0•1•0•Updated Mar 21, 2023Mar 21, 2023