Alternatives and similar repositories for lineage-proposals

Users that are interested in lineage-proposals are comparing it to the libraries listed below

• neherlab / SARS-CoV-2_variant-reports
  Informal summaries of notable SARS-CoV-2 lineages
  ☆110Updated 3 months ago
• Memorablea / COVID-19-
  ☆11Updated last year
• cov-lineages / pangolin
  Software package for assigning SARS-CoV-2 genome sequences to global lineages.
  ☆443Updated last month
• nextstrain / nextclade
  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
  ☆250Updated this week
• yatisht / usher
  Ultrafast Sample Placement on Existing Trees
  ☆138Updated last month
• W-L / ProblematicSites_SARS-CoV2
  ☆50Updated 3 years ago
• nextstrain / nextclade_data
  Datasets for https://github.com/nextstrain/nextclade
  ☆42Updated this week
• ncbi / vadr
  Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
  ☆111Updated last week
• nextstrain / mpox
  Nextstrain build for mpox virus
  ☆50Updated last week
• cov-lineages / pangoLEARN
  Store of the trained model for pangolin to access.
  ☆55Updated 3 years ago
• andersen-lab / Freyja
  Depth-weighted De-Mixing
  ☆125Updated this week
• MurrellGroup / lineages
  Results from a model of global SARS-CoV-2 lineage competition
  ☆39Updated 3 months ago
• evogytis / baltic
  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…
  ☆114Updated this week
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆32Updated last month
• cov-lineages / pango-designation
  Repository for suggesting new lineages that should be added to the current scheme
  ☆1,070Updated this week
• mdmparis / defense-finder
  Systematic search of all known anti-phage systems.
  ☆132Updated 2 months ago
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated 2 years ago
• lenaschimmel / sc2rf
  SARS-Cov-2 Recombinant Finder for fasta sequences
  ☆50Updated 3 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 7 months ago
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated this week
• nextstrain / ncov-clades-schema
  Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
  ☆16Updated 3 weeks ago
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆248Updated last week
• santa-dev / santa-sim
  A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
  ☆20Updated 2 years ago
• biobakery / graphlan
  High-quality circular representations of taxonomic and phylogenetic trees
  ☆105Updated last year
• soedinglab / spacedust
  Discovery of conserved gene clusters in multiple genomes
  ☆119Updated 7 months ago
• corneliusroemer / pango-sequences
  Consensus sequences for each Pango lineage
  ☆22Updated 5 months ago
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated 2 years ago
• GSLBiotech / mafft
  Align multiple amino acid or nucleotide sequences.
  ☆66Updated 5 years ago
• EddyRivasLab / infernal
  RNA secondary structure/sequence profiles for homology search and alignment
  ☆119Updated last year
• KennthShang / PhaGCN2.0
  ☆35Updated 5 months ago