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
  ☆198Updated this week
• Cibiv / IQ-TREE
  Efficient phylogenomic software by maximum likelihood
  ☆191Updated 3 years ago
• stamatak / standard-RAxML
  ☆333Updated 5 months ago
• beagle-dev / beagle-lib
  general purpose library for evaluating the likelihood of sequence evolution on trees
  ☆132Updated 3 weeks ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆301Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆216Updated 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…
  ☆238Updated 4 months ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆231Updated 2 months ago
• amkozlov / raxml-ng
  RAxML Next Generation: faster, easier-to-use and more flexible
  ☆405Updated this week
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆369Updated last year
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆261Updated this week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆206Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆182Updated 11 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆231Updated last year
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆233Updated 9 months ago
• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆270Updated 2 months ago
• MesquiteProject / MesquiteCore
  The core Mesquite repository
  ☆100Updated this week
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆298Updated 5 months ago
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆180Updated last week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆345Updated 2 years ago
• AliView / AliView
  Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:
  ☆120Updated 3 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆329Updated this week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆313Updated 7 months ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆115Updated last week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆204Updated this week
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆159Updated 2 years ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆276Updated this week
• smirarab / ASTRAL
  Accurate Species TRee ALgorithm
  ☆250Updated 9 months ago
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆233Updated 2 weeks ago
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆136Updated 2 years ago