Alternatives and similar repositories for compare_genomes:

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

• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆31Updated 2 years ago
• lauguma / GWideCodeML
  A Python package for testing evolutionary hypotheses in genome-wide approaches.
  ☆31Updated 3 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
• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆33Updated 6 years ago
• JLSteenwyk / PhyKIT
  a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
  ☆67Updated last month
• HuffordLab / GenomeQC
  ☆32Updated 4 years ago
• harta55 / EnTAP
  EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP
  ☆38Updated last week
• obenno / ShinySyn
  A shiny application to visualize MCscan result
  ☆34Updated 2 years ago
• rderelle / Broccoli
  orthology assignment using phylogenetic and network analyses
  ☆46Updated 3 months ago
• schneebergerlab / findGSE
  findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a ske…
  ☆36Updated last year
• heche-psb / wgd
  wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
  ☆29Updated last month
• ThomasArn / genoPlotR_wrapper
  Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR p…
  ☆14Updated 3 years ago
• Gaius-Augustus / Tiberius
  Tiberius is a deep learning gene finder.
  ☆46Updated this week
• lh3 / calN50
  Compute N50/NG50 and auN/auNG
  ☆31Updated last year
• h836472 / ContScout
  ContScout sequence contamination filter tool
  ☆19Updated 2 weeks ago
• i10labtitech / GINGER
  ☆27Updated last year
• sjspielman / phyphy
  Python HyPhy: Facilitating HyPhy execution and parsing
  ☆21Updated 3 years ago
• SamiLhll / macrosyntR
  R package for comparison of synteny conservation at the genome-wide scale.
  ☆14Updated 7 months ago
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆35Updated 9 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• Plant-Food-Research-Open / assemblyqc
  A Nextflow pipeline for evaluating assembly quality
  ☆28Updated last month
• popgenmethods / SINGER
  Sampling and inference of genealogies with recombination
  ☆29Updated 4 months ago
• DessimozLab / FastOMA
  FastOMA is a scalable software package to infer orthology relationship.
  ☆64Updated this week
• PombertLab / SYNY
  The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
  ☆40Updated 3 weeks ago
• Dee-chen / Tree2gd
  ☆39Updated 2 years ago
• Rinoahu / SwiftOrtho
  A high performance tool to identify orthologs and paralogs across genomes.
  ☆27Updated last year
• gengit / PosiGene
  ☆26Updated 3 years ago
• JLSteenwyk / orthosnap
  a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
  ☆25Updated last month
• slimsuite / chromsyn
  Chromosome-level synteny plotting using orthologous regions
  ☆28Updated 4 months ago
• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆30Updated last month