Alternatives and similar repositories for SNPhylo

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

• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆87Updated 3 years ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆114Updated 10 months ago
• steuernb / NLR-Annotator
  NLR-Annotator upload
  ☆71Updated 2 years ago
• hardingnj / xpclr
  Code to compute the XP-CLR statistic to infer natural selection
  ☆98Updated 3 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• BGI-shenzhen / VCF2Dis
  VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Forma…
  ☆97Updated 3 months ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 8 years ago
• 4ureliek / Parsing-RepeatMasker-Outputs
  Few scripts facilitating the extraction of info from Repeat Masker .out files
  ☆81Updated 4 years ago
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆80Updated last year
• arzwa / wgd
  Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…
  ☆85Updated last year
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆104Updated 3 months ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆58Updated 2 years ago
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆109Updated last year
• Trinotate / Trinotate.github.io
  web documentation for Trinotate
  ☆48Updated 2 years ago
• stevemussmann / admixturePipeline
  A pipeline that accepts a VCF file to run through Admixture
  ☆62Updated 7 months ago
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆99Updated 6 months ago
• nt246 / lcwgs-guide-tutorial
  ☆90Updated 3 years ago
• rhysf / Synima
  Synteny Imager
  ☆64Updated last month
• szpiech / selscan
  Haplotype based scans for selection
  ☆131Updated this week
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Updated 3 years ago
• xiaochuanle / MECAT2
  ☆71Updated 5 years ago
• hyphaltip / genome-scripts
  Genome Scripts used in fungal comparative genomics
  ☆67Updated 4 years ago
• tonig-evo / workshop-popgenome
  Tutorial about R package PopGenome
  ☆43Updated 6 years ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆106Updated 2 months ago
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆116Updated 9 months ago
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆100Updated last week
• bmansfeld / QTLseqr
  QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
  ☆80Updated 5 years ago
• MikkelSchubert / paleomix
  Pipelines and tools for the processing of ancient and modern HTS data.
  ☆47Updated 2 weeks ago
• nclark-lab / RERconverge
  Analysis of convergence between organismal traits and DNA/protein sequences
  ☆57Updated 3 weeks ago