polyploidy

There are 0 repository under polyploidy topic.

• SunPengChuan / wgdi

  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

  ancestral-chromosomal-karyotypebioinformaticscollinearitypolyploidy
  Language:Python 123

• arzwa / wgd

  Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.

  wgdduplicationpolyploidybioinformaticsgenomicsevolution
  Language:Python 84
• MAPpoly

  mmollina / MAPpoly

  Genetic maps in autopolyploids

  polyploidpolyploid-genetic-mappingpolyploidy
  Language:R 26

• PlantandFoodResearch / MCHap

  Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

  dna-sequenceshaplotypeshaplotype-assemblyhaplotype-blocksarraynumpybayesian-inferencepolyploidypolyploid-genotypinggenotyping
  Language:Python 18

• hannesbecher / shiny-k-mers

  Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)

  allotetraploidybioinformaticsgenome-sizek-mer-spectrumk-merskmersploidy-inferencepolyploidytetmer
  Language:R 13

• almeidasilvaf / HybridExpress

  An R package for comparative transcriptomic analyses of hybrids and their progenitors

  gene-expressionhybridpolyploidyrna-seqtranscriptomics
  Language:R 12

• arzwa / Whale.jl

  Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

  phylogeneticsreconciliationwgdpolyploidybioinformaticsgenomicsevolutionmcmcbayesian
  Language:Julia 12

• gwct / grampa

  Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis

  phylogeneticsbioinformaticspolyploidy
  Language:Python 11

• mgaynor1 / nQuack

  An R package for predicting ploidal level from sequence data using site-based heterozygosity 

  rcpprcpparmadilloexpectation-maximizationpolyploidyr-based
  Language:C++ 11

• lauzingaretti / pSBVB

  Manual

  genotypepolyploidysnps
  Language:Roff 10

• plantarum / flowPloidy

  An R package for flow cytometry histogram analysis

  bioconductorflow-cytometryevolutionpolyploidy
  Language:R 5

• almeidasilvaf / doubletroubledb

  A dashboard to explore and download the duplicated gene repertoire in eukaryote species

  evolutionary-genomicsgene-duplicationgenome-duplicationpolyploidyquarto-dashboardrstats
  Language:R 4

• mgaynor1 / AutoPop

  R-based autopolyploid population and population genetic simulation

  autopolyploidypolyploidyr-based
  Language:R 4

• alethere / mpQTL

  github repository for R package mpQTL

  haplotypepolyploidyqtl-mapping
  Language:R 3

• Genome-structure-evolution-analysis / AKRUP

  AKRUP: ancestral karyotype reconstruction universal pipeline

  ancestral-chromosomal-karyotypebioinformaticsblastpolyploidysynteny
  Language:Python 3

• rosemckeon / ploidy

  How does disturbance on a landscape affect the establishment of new polyploid plant species?

  disturbanceecologyevolutiongeneticsindividual-based-modellingplantspolyploidyr
  Language:R 3

• almeidasilvaf / HybridExpress_paper

  Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"

  heterosishybridspolyploidyreproducible-researchrna-seqtranscriptomics
  Language:JavaScript 1

• Glfrey / Hijacking_Sourmash

  Scripts, information and data for publication in APPS.

  bioinformaticsmetagenomicspolyploidy
  Language:Python 1

• kemcelroy / Pant_rDNAhistones

  Bioinformatic methods used in McElroy et al. (2021). Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes. Molecular Biology and Evolution.

  genomicsasexual-reproductionpolyploidyrepetitive-elementsrdna
  1

• rlbaker5 / polyploidy_networks

  Script and data supporting a Brassica network analysis manuscript submitted to Applications in Plant Sciences

  brassicaevolutionnetwork-analysisphenotypic-integrationpolyploidyr
  Language:R 0

• jnarayan81 / Polyploidism

  Estimate the polyploidy

  ploidyestimategenomepolyploidy
  Language:C++

• szhan / inst-spec

  R scripts and data files to test the "instant speciation" hypothesis

  diversification-ratepolyploidy
  Language:R