Alternatives and similar repositories for beast2:

Users that are interested in beast2 are comparing it to the libraries listed below

• beast-dev / beast-mcmc
  Bayesian Evolutionary Analysis Sampling Trees
  ☆202Updated this week
• beagle-dev / beagle-lib
  general purpose library for evaluating the likelihood of sequence evolution on trees
  ☆134Updated this week
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆185Updated 2 weeks ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆222Updated 2 years ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆308Updated last year
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆241Updated last year
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆135Updated 2 years ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆278Updated 3 months ago
• marbl / Mash
  Fast genome and metagenome distance estimation using MinHash
  ☆403Updated last year
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆380Updated last year
• stamatak / standard-RAxML
  ☆339Updated last month
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆240Updated last year
• NBISweden / MrBayes
  MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentati…
  ☆242Updated last week
• ANGSD / angsd
  Program for analysing NGS data.
  ☆236Updated last month
• ddarriba / modeltest
  Best-fit model selection
  ☆80Updated last year
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆342Updated 3 years ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆307Updated last month
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆199Updated 8 months ago
• nf-core / eager
  A fully reproducible and state-of-the-art ancient DNA analysis pipeline
  ☆165Updated last week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆319Updated 10 months ago
• mfumagalli / ngsTools
  Programs to analyse NGS data for population genetics purposes
  ☆174Updated 7 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆357Updated 3 years ago
• sanger-pathogens / ariba
  Antimicrobial Resistance Identification By Assembly
  ☆174Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆187Updated last year
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆240Updated last month
• iqtree / iqtree2
  IQ-TREE software version 2: phylogenetics by maximum likelihood
  ☆281Updated last week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆210Updated this week
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆121Updated 3 months ago
• loneknightpy / idba
  ☆127Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆114Updated last month