Alternatives and similar repositories for SimPhy

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

• mrmckain / Fast-Plast
  Automated de novo assembly of whole chloroplast genomes.
  ☆47Updated last year
• clwgg / nQuire
  A statistical framework for ploidy estimation using NGS short-read data
  ☆62Updated 7 years ago
• mfoll / BayeScan
  Detecting natural selection from population-based genetic data
  ☆28Updated 6 years ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• stschiff / msmc2
  ☆65Updated 2 years ago
• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆50Updated last year
• MikkelSchubert / paleomix
  Pipelines and tools for the processing of ancient and modern HTS data.
  ☆47Updated 2 weeks ago
• stschiff / msmc
  Implementation of the multiple sequential markovian coalescent
  ☆89Updated 3 months ago
• sjspielman / phyphy
  Python HyPhy: Facilitating HyPhy execution and parsing
  ☆21Updated 3 years ago
• esayyari / DiscoVista
  ☆42Updated 2 years ago
• ddarriba / prottest3
  Automatically exported from code.google.com/p/prottest3
  ☆38Updated 7 years ago
• bcgsc / tigmint
  ⛓ Correct misassemblies using linked AND long reads
  ☆63Updated 2 years ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆75Updated 4 years 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
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• arangrhie / merfin
  Evaluate variant calls and its combination with k-mer multiplicity
  ☆67Updated 2 years ago
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆36Updated last year
• lh3 / unimap
  A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
  ☆87Updated 4 years ago
• darwintreeoflife / darwintreeoflife.data
  Interim data for the Darwin Tree of Life Project
  ☆33Updated 5 years ago
• auton1 / LDhat
  Estimate recombination rates from population genetic data
  ☆69Updated 5 years ago
• lutteropp / QuartetScores
  Code for computing various support scores for internodes
  ☆19Updated 5 years ago
• cboursnell / crb-blast
  Conditional Reciprocal Best Blast
  ☆42Updated 8 years ago
• hillerlab / GenomeAlignmentTools
  Tools for improving the sensitivity and specificity of genome alignments
  ☆58Updated last year
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆59Updated 2 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆74Updated 3 months ago
• GATB / gatb-minia-pipeline
  GATB Minia assembly pipeline
  ☆31Updated 2 years ago
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆48Updated 2 weeks ago
• NakhlehLab / PhyloNet
  ☆21Updated last month
• josephryan / estimate_genome_size.pl
  Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
  ☆57Updated 2 years ago
• Sun-Yanbo / FasParser
  A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data
  ☆30Updated 4 years ago