Alternatives and similar repositories for augur

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

• nextstrain / nextclade
  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
  ☆247Updated this week
• ababaian / serratus
  Ultra-deep search for novel viruses
  ☆272Updated 2 years ago
• sourmash-bio / sourmash
  Quickly search, compare, and analyze genomic and metagenomic data sets.
  ☆524Updated last week
• stephaneguindon / phyml
  PhyML -- Phylogenetic estimation using (Maximum) Likelihood
  ☆193Updated last month
• merenlab / anvio
  An analysis and visualization platform for 'omics data
  ☆488Updated 2 weeks ago
• galaxyproject / SARS-CoV-2
  Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures
  ☆127Updated 2 years ago
• veg / hyphy
  HyPhy: Hypothesis testing using Phylogenies
  ☆243Updated this week
• nextstrain / auspice
  Web app for visualizing pathogen evolution
  ☆304Updated this week
• broadinstitute / viral-ngs
  [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …
  ☆195Updated last year
• ncbi / amr
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…
  ☆329Updated last month
• sanger-pathogens / Artemis
  Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the…
  ☆258Updated last year
• cov-lineages / pangolin
  Software package for assigning SARS-CoV-2 genome sequences to global lineages.
  ☆444Updated 2 weeks ago
• bcgsc / NanoSim
  Nanopore sequence read simulator
  ☆284Updated 8 months ago
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆326Updated 7 months ago
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆247Updated this week
• ncbi / blast_plus_docs
  ☆117Updated 2 years ago
• galaxyproject / tools-iuc
  Tool Shed repositories maintained by the Intergalactic Utilities Commission
  ☆182Updated this week
• bioSyntax / bioSyntax
  Syntax highlighting for computational biology
  ☆269Updated 2 years ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆480Updated this week
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆400Updated last month
• ncbi / vadr
  Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
  ☆109Updated last month
• sanger-pathogens / ariba
  Antimicrobial Resistance Identification By Assembly
  ☆181Updated 2 years ago
• Ecogenomics / GTDBTk
  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
  ☆550Updated this week
• nextstrain / seasonal-flu
  Scripts. config, and snakefiles for seasonal-flu nextstrain builds
  ☆53Updated this week
• VoigtLab / dnaplotlib
  DNA plotting library for Python
  ☆299Updated last year
• chanzuckerberg / czid-web
  Infectious Disease Sequencing Platform
  ☆86Updated 2 weeks ago
• CDCgov / SARS-CoV-2_Sequencing
  A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
  ☆349Updated 2 years ago
• jeetsukumaran / DendroPy
  A Python library for phylogenetic scripting, simulation, data processing and manipulation.
  ☆223Updated 2 weeks ago
• evogytis / baltic
  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…
  ☆112Updated last month
• ncbi / datasets
  NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
  ☆474Updated last month