Alternatives and similar repositories for pastml

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

• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆32Updated 3 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• gtonkinhill / rhierbaps
  rhierbaps: R implementation of hierBAPS
  ☆35Updated 4 years ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆43Updated 2 years ago
• computations / root_digger
  A tool to root phylogenies
  ☆23Updated last year
• dhelekal / CaveDive
  ☆18Updated last year
• marekborowiec / spruceup
  spruceup
  ☆25Updated 3 months ago
• blackrim / phyutility
  ☆22Updated 11 years ago
• balabanmetin / uDance
  ☆42Updated last year
• arzwa / Whale.jl
  Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation
  ☆16Updated 6 months ago
• ranwez / MACSE_V2_PIPELINES
  This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…
  ☆35Updated 2 years ago
• emvolz / treedater
  Scalable relaxed clock phylogenetic dating
  ☆27Updated 2 months ago
• sjspielman / phyphy
  Python HyPhy: Facilitating HyPhy execution and parsing
  ☆21Updated 3 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• ballesterus / Utensils
  Simple scripts for concatenate alignments and rename terminals for phylogenetics
  ☆22Updated 3 years ago
• NicolaDM / MAPLE
  MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.
  ☆56Updated 3 weeks ago
• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆50Updated last year
• gwct / referee
  Reference genome quality scores
  ☆21Updated 4 years ago
• rnajena / poseidon
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆38Updated last month
• danny-wilson / genomegaMap
  Within-species genome-wide dN/dS estimation from very many genomes
  ☆21Updated 5 years ago
• dportik / SuperCRUNCH
  A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local seq…
  ☆44Updated last year
• shahab-sarmashghi / Skmer
  Fast and accurate tool for estimating genomic distances between genome-skims
  ☆45Updated 2 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• ktrappe / daisy
  Horizontal Gene Transfer Detection by Mapping Sequencing Reads
  ☆21Updated 8 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• BenoitMorel / Asteroid
  ☆15Updated last year
• gengit / PosiGene
  ☆26Updated 4 years ago
• PuttickMacroevolution / MCMCtreeR
  MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree
  ☆45Updated 5 years ago
• kr-colab / locator
  deep learning prediction of geographic location from individual genome sequences
  ☆51Updated 9 months ago