recombination

There are 1 repository under recombination topic.

• kr-colab / ReLERNN

  Recombination Landscape Estimation using Recurrent Neural Networks

  population-genomicsdeep-learningrecurrent-neural-networksrecombination
  Language:Python 62

• vinuesa / get_phylomarkers

  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

  phylogenomicspopulation-geneticsphylogenomics-pipelinespecies-treesmarkersgenomicspipelinephylogeneticsphylogenetic-treescodon-alignmentmaximum-likelihoodorthologuesspecies-delimitationmicrobiologycore-genomeperlrbashclock-hypothesisrecombination
  Language:Perl 59

• qmarcou / IGoR

  IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

  inferenceigorrecombinationimmunologysimulationhypermutation
  Language:C 51

• kr-colab / discoal

  discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

  admixture-eventsdemographic-changesrecombinationselective-sweepssimulation-model
  Language:TeX 49

• kussell-lab / mcorr

  Inferring bacterial recombination rates from large-scale sequencing datasets.

  correlationrecombination
  Language:Go 42

• solgenomics / SNPbinner

  SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

  bioinformaticsanalysissnpsnp-datarecombinationgenotypehmm
  Language:Python 37

• beiko-lab / arete

  AMR/VF LGT focused bacterial genomics analysis workflow

  antimicrobial-resistancebacterial-genome-analysislateral-gene-transfermetagenomicsantimicrobial-genes-annotationgenomic-islands-predictionmobile-genetic-elementsnextflowpangenomicspipelinepoppunkrecombinationreproducible-researchrgivirulence-factor
  Language:Python 27
• idplot

  brwnj / idplot

  compare sequences to a shared root reference sequence.

  fastanextflowplotlyrecombinationsars-cov-2virus
  Language:HTML 24

• ktmeaton / ncov-recombinant

  Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

  sars-cov-2recombinationrecombinantgenomicsncov
  Language:Python 18

• kussell-lab / viral-mcorr

  Using correlated substitutions to infer recombination rates in RNA viruses

  coronavirusrecombinationsars-cov-2viruses
  Language:Go 17

• WMD-group / StarryNight

  Monte Carlo codes to simulate polar domains in hybrid perovskite solar cells

  monte-carlo-codesferroelectric-domainsperovskitephotovoltaicmonte-carlodipole-domainsrecombinationsemiconductor
  Language:C 16

• phac-nml / rebar

  REcombination BARcode detector.

  recombinationrustsars-cov-2
  Language:Rust 13

• PierreBarrat / TreeKnit.jl

  TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).

  argphylogenyrecombinationreassortment
  Language:Julia 13

• simhag / Compositional-Pre-Training-for-Semantic-Parsing-with-BERT

  Implementation of Semantic Parsing with BERT and compositional pre-training on GeoQuery

  semantic-parsingnatural-language-processingberttransformerrecombinationcompositional-data
  Language:Scala 11

• phylo42 / sherpas

  Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

  virusrecombinationsubtypinggenotypingkmersphylo-kmersrecombination-detectionancestral-sequences
  Language:C++ 9

• fanglab / BEAST

  Bacterial Epigenomics Analysis SuiTe

  bacteriaepigeneticsmethylationrna-seqsmrttfbs-discoverydifferential-expressionunix-shellhgtrecombination
  Language:R 8

• mtekman / HaploForge

  HTML5 pedigree/haplotype explorer, featuring a rich selection of comparison tools.

  haplotype-applicationsrecombinationvisualizationfounder-allelephased-genotypeshtml5kineticjs
  Language:JavaScript 8
• RecombineX

  yjx1217 / RecombineX

  A computational framework for tetrad-based genotyping & recombination landscape analysis

  tetradrecombinationmeiosisspore
  Language:Perl 8
• haploMAGIC

  GoliczGenomeLab / haploMAGIC

  Phasing, haplotype reconstruction and crossover detection with single-nucleotide polymorphism data from multiparental populations.

  breedinggenomicsrrecombinationsnp
  Language:R 6

• pangenome / chromosome_communities

  Recombination between heterologous human acrocentric chromosomes

  pangenomerecombinationtranslocation
  Language:R 6

• tkchafin / FGTpartitioner

  Parsimonious delimitation of large SNP datasets using the four gamete test

  genome-alignmentrecombinationancestryphylogenomics
  Language:Python 6

• drostlab / retrocombinator

  An R/C++ package for simulating the evolution of retrotransposons over time.

  evolutionrecombinationretrotransposonsspeciationtransposable-elementtranspositiontransposons
  Language:HTML 4

• HKyleZhang / RecView

  view and locate recombinations positions using pedigree data

  recombinationgenomicsgeneticsrshinyapp
  Language:R 4

• Ping-Group-UCSC / NonRad

  This code computes the nonradiative recombination at defect centers from first-principles

  nonradiativerecombinationfirst-principles
  Language:Python 4

• alfonsomiguelcruz / pgc_btip_topone

  TopONE is a project that studies recombination events using topological data analysis. This was made in the PGC-BTIP 2024 internship by Alfonso Miguel Cruz and Claire Angelie Gabisay, and mentored by C.J. Palpal-latoc.

  bioinformaticsbioinformatics-scriptsmsrecombinationrecombination-eventssars-cov-2topological-data-analysistopologygenomicsviral-genomics
  Language:Python 3

• zzsfornlp / znmt-merge

  NMT decoding with recombination (merging).

  decodingnmtrecombination
  Language:Python 3

• manu-script / recomb_landscape

  Codes and Datasets used in the manuscript titled "Systematic Analyses of Autosomal Recombination Rates from the 1000 Genomes Project Uncovers the Global Recombination Landscape in Humans."

  evolutionary-computationrecombination
  Language:Python 2

• alipirani88 / find_hgt_pipeline

  compare multiple fasta files using nucmer and extract aligned fragments

  bioinformaticsnucmerrecombinationhgt
  Language:Python 1

• AnimaTardeb / Meiogenix-UGDR

  UGDR: a pipeline to detect and analyze recombination in yeast.

  allele-variationyeastrecombined-genomesrecombinationpython
  Language:Python 1

• cmkobel / gBGC

  🦠💪 Investigating gBGC in Rhizobium leguminosarum

  msc-thesismicrobiologyrecombination
  Language:Python 1

• dennishazelett / recombulator

  Calculate recombination frequencies and plan for crosses in Drosophila Genetics

  geneticsdrosophilarecombination
  Language:Python 1

• FraCose / Recombination_Random_Algos

  Cosentino, Oberhauser, Abate - A randomized algorithm to reduce the support of discrete measures

  recombinationprobability
  Language:Jupyter Notebook 1

• MafaldaSFerreira / Atlherr_inversion_evol

  Evolutionary genomics of chromosomal inversions in Atlantic herring

  dnds-estimationdxyevolutionary-biologyfstgatk4genomicsgenotypeinversionslong-readsnucleotide-diversitypcaphylogenomicsrecombinationshort-readssite-frequency-spectrumtransposable-elementswhole-genome-alignment
  Language:R 1

• scikal / LD-CHASE

  A tool for linkage disequilibrium-informed comparison of haplotypes among sibling embryos.

  recombinationcrossoverslinkage-disequilibriumreference-panel
  Language:Python 1

• lightning-auriga / interpolate-genetic-position

  Use reference genetic map to interpolate genetic position for a query set of variants

  gwaspopulation-geneticsrecombinationstatistical-genetics
  Language:C++ 0

• mbursell / ReLERNN-pipeline

  recombinationrelernn
  Language:Shell 0