Alternatives and similar repositories for Quantification-of-the-spread-of-a-SARS-CoV-2-variant

Users that are interested in Quantification-of-the-spread-of-a-SARS-CoV-2-variant are comparing it to the libraries listed below

• theosanderson / chronumental
  Estimating time trees from very large phylogenies
  ☆26Updated 11 months ago
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• mrc-ide / skygrowth
  Phylodynamic inference
  ☆18Updated 5 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆35Updated 3 weeks ago
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆76Updated 2 months ago
• sdellicour / seraphim
  R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.…
  ☆35Updated 2 months ago
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated last year
• abschneider / StrainHub
  Welcome to the StrainHub Repo - Files and Data - StrainHub Online:
  ☆17Updated 3 years ago
• MetaSUB / MetaSUB_CAP
  A comprehensive pipeline for short read metagenomic data
  ☆24Updated 4 years ago
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆86Updated last year
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 3 weeks ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆56Updated 9 months ago
• broadinstitute / beast-beagle-cuda
  BEAST+BEAGLE compiled with NVIDIA CUDA
  ☆10Updated 11 months ago
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• yangfangs / physpetools
  PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
  ☆14Updated last year
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated last year
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• nodrogluap / pokay
  Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes
  ☆14Updated 3 months ago
• flu-crew / TreeSort
  Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
  ☆15Updated 2 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆62Updated 2 years ago
• covince / covince
  Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.
  ☆10Updated 2 years ago
• ryanmelnyk / PyParanoid
  Rapid and scalable homolog identification for bacterial genomes
  ☆32Updated 5 years ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• danlwarren / RWTY
  R We There Yet?
  ☆30Updated 3 months ago
• metageni / SUPER-FOCUS
  A tool for agile functional analysis of shotgun metagenomic data
  ☆24Updated 9 months ago
• katholt / plotTree
  ☆67Updated 8 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated 2 months ago
• acorg / Racmacs
  Racmacs R package for performing antigenic cartography
  ☆23Updated last year
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆27Updated this week
• tgvaughan / MASTER
  A versatile simulation engine for stochastic population dynamics models.
  ☆22Updated 2 years ago