Alternatives and similar repositories for lineages

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

• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated last year
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated last week
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆85Updated 2 years ago
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated 2 years ago
• grubaughlab / DENV_pipeline
  ☆19Updated 7 months ago
• W-L / ProblematicSites_SARS-CoV2
  ☆50Updated 3 years ago
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated last week
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 2 months ago
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• salzberg-lab / Balrog
  Bacterial Annotation by Learned Representation of Genes
  ☆58Updated 4 years ago
• nextstrain / mpox
  Nextstrain build for mpox virus
  ☆50Updated last week
• Ebedthan / xgt
  Efficient and fast querying and parsing of GTDB's data
  ☆29Updated 3 months ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 5 months ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated last month
• evogytis / baltic
  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…
  ☆112Updated last 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
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆58Updated last week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 2 months ago
• mdmparis / defense-finder-models
  MacSyFinder models allowing for a systematic search of anti-phage systems
  ☆23Updated 9 months ago
• theosanderson / taxonium
  A tool for exploring large trees in the browser
  ☆118Updated 2 weeks ago
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆32Updated 2 weeks ago
• steineggerlab / unicore
  Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
  ☆78Updated 2 weeks ago
• metagenlab / locus2genoplotr
  Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
  ☆12Updated last year
• kelwyres / Bactabolize
  ☆41Updated 5 months ago
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆70Updated 3 weeks ago
• corneliusroemer / pango-sequences
  Consensus sequences for each Pango lineage
  ☆22Updated 5 months ago
• bhattlab / phanta
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
  ☆66Updated 2 months ago
• shandley / awesome-virome
  A listing of software, tools and databases useful for virome analysis
  ☆53Updated this week
• tothuhien / lsd2
  A phylogeny dating method using least-squares algorithms and criteria
  ☆30Updated last year
• Arcadia-Science / 2023-nr-clustering
  Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.
  ☆23Updated 3 weeks ago