Alternatives and similar repositories for lineages

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

• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated 2 years ago
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated 2 years ago
• grubaughlab / DENV_pipeline
  ☆20Updated 8 months ago
• W-L / ProblematicSites_SARS-CoV2
  ☆50Updated 3 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆38Updated 2 months ago
• 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 8 months ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆60Updated 3 weeks ago
• nextstrain / mpox
  Nextstrain build for mpox virus
  ☆50Updated last week
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated last month
• corneliusroemer / pango-sequences
  Consensus sequences for each Pango lineage
  ☆22Updated 5 months ago
• lenaschimmel / sc2rf
  SARS-Cov-2 Recombinant Finder for fasta sequences
  ☆50Updated 3 years ago
• baymlab / wastewater_analysis
  Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
  ☆15Updated 2 years ago
• deprekate / PHANOTATE
  PHANOTATE: a gene caller for phages.
  ☆79Updated last year
• nextstrain / avian-flu
  Nextstrain build for avian influenza viruses
  ☆27Updated this week
• steineggerlab / unicore
  Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
  ☆80Updated last month
• tothuhien / lsd2
  A phylogeny dating method using least-squares algorithms and criteria
  ☆32Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 2 months ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated last week
• theosanderson / taxonium
  A tool for exploring large trees in the browser
  ☆119Updated last week
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆48Updated 2 weeks ago
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated this week
• evogytis / baltic
  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…
  ☆114Updated this week
• flu-crew / TreeSort
  Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
  ☆20Updated 2 months ago
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆32Updated last month
• Vini2 / phables
  🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
  ☆81Updated 2 weeks ago
• theosanderson / chronumental
  Estimating time trees from very large phylogenies
  ☆28Updated last year
• kelwyres / Bactabolize
  ☆42Updated 6 months ago
• NicolaDM / MAPLE
  MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.
  ☆57Updated last month
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆87Updated 3 years ago
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆31Updated 3 months ago