Alternatives and similar repositories for beagle-lib:

Users that are interested in beagle-lib are comparing it to the libraries listed below

• AliView / AliView
  Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:
  ☆120Updated 3 months ago
• CompEvol / beast2
  Bayesian Evolutionary Analysis by Sampling Trees
  ☆245Updated this week
• beast-dev / beast-mcmc
  Bayesian Evolutionary Analysis Sampling Trees
  ☆198Updated this week
• 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
• ddarriba / modeltest
  Best-fit model selection
  ☆79Updated 9 months ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆115Updated last week
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆233Updated 9 months ago
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆180Updated last week
• ANGSD / angsd
  Program for analysing NGS data.
  ☆231Updated 2 months ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆182Updated 11 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆128Updated 10 months ago
• stamatak / standard-RAxML
  ☆333Updated 5 months ago
• isovic / graphmap
  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…
  ☆180Updated 5 years ago
• barricklab / breseq
  breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inte…
  ☆154Updated 2 weeks ago
• beast-dev / tracer
  Posterior summarisation in Bayesian phylogenetics
  ☆57Updated 4 months ago
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆136Updated 2 years ago
• Gabaldonlab / redundans
  Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
  ☆134Updated last year
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆313Updated 7 months ago
• abacus-gene / paml
  PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…
  ☆137Updated last month
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆110Updated last year
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆111Updated 7 months ago
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆233Updated 2 weeks ago
• widdowquinn / pyani
  Application and Python module for average nucleotide identity analyses of microbes.
  ☆200Updated 3 months ago
• FePhyFoFum / phyx
  phylogenetics tools for linux (and other mostly posix compliant) computers
  ☆117Updated this week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆110Updated last week
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆231Updated last year
• CAMI-challenge / CAMISIM
  CAMISIM: Simulating metagenomes and microbial communities
  ☆188Updated 5 months ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆115Updated 3 years ago
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆261Updated this week