Alternatives and similar repositories for mpox

Users that are interested in mpox are comparing it to the libraries listed below

• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated last month
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆32Updated last month
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 4 months ago
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated this week
• W-L / ProblematicSites_SARS-CoV2
  ☆50Updated 3 years ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated 2 years ago
• theosanderson / chronumental
  Estimating time trees from very large phylogenies
  ☆28Updated last year
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated last year
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆78Updated 2 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
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated 2 years ago
• yatisht / usher
  Ultrafast Sample Placement on Existing Trees
  ☆134Updated this week
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆58Updated 7 months ago
• lenaschimmel / sc2rf
  SARS-Cov-2 Recombinant Finder for fasta sequences
  ☆50Updated 3 years ago
• nextstrain / nextclade_data
  Datasets for https://github.com/nextstrain/nextclade
  ☆41Updated this week
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆85Updated 2 years ago
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆40Updated 3 weeks ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆38Updated last week
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• grubaughlab / DENV_pipeline
  ☆18Updated 7 months ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 6 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• gtonkinhill / rhierbaps
  rhierbaps: R implementation of hierBAPS
  ☆35Updated 4 years ago
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆57Updated 2 years ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆59Updated last year
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆115Updated this week
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆57Updated this week
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆58Updated 2 weeks ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 3 years ago
• pirovc / ganon
  ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…
  ☆102Updated 6 months ago