Alternatives and similar repositories for lineage-designation:

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

• theosanderson / chronumental
  Estimating time trees from very large phylogenies
  ☆25Updated 6 months ago
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆22Updated last year
• mrc-ide / skygrowth
  Phylodynamic inference
  ☆18Updated 4 years ago
• grubaughlab / DENV_pipeline
  ☆15Updated last week
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆29Updated this week
• nextstrain / zika-tutorial
  Data and scripts for Zika virus tutorial
  ☆10Updated last month
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆27Updated this week
• emvolz-phylodynamics / treestructure
  ☆17Updated 8 months ago
• emvolz / treedater
  Scalable relaxed clock phylogenetic dating
  ☆24Updated 10 months ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 2 years ago
• CDCgov / aquascope
  ☆20Updated last week
• emvolz-phylodynamics / mlesky
  ☆10Updated 9 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆32Updated last month
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated last year
• noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
  Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
  ☆12Updated 3 months ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆61Updated last year
• bdearlove / Phylogeography-in-BEAST
  Inferring spatiotemporal dynamics of H5N1 influenza from sequence data
  ☆9Updated 10 years ago
• ktmeaton / ncov-recombinant
  Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
  ☆18Updated last year
• chrisruis / bammix
  Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures
  ☆13Updated 2 years ago
• tothuhien / lsd-0.3beta
  ☆12Updated 5 years ago
• duchene / phylomad
  ☆19Updated 7 months ago
• sdellicour / seraphim
  R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.…
  ☆30Updated last week
• phytest-devs / phytest
  Quality control for phylogenetic analyses
  ☆13Updated 3 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆34Updated last week
• tothuhien / Rlsd2
  An R-wrapper for lsd2
  ☆9Updated last year
• neherlab / treetime_examples
  A collection of documented examples using TreeTime
  ☆20Updated 5 years ago
• jsigao / prioritree
  ☆9Updated 2 years ago
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆31Updated this week
• chienchi / amplicon_coverage_plot
  interactive barplot for amplicon sequencing
  ☆13Updated last month
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated last month