Alternatives and similar repositories for GAPIT

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

• BGI-shenzhen / LDBlockShow
  LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
  ☆197Updated 6 months ago
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆201Updated last year
• TickingClock1992 / RIdeogram
  ☆190Updated 5 years ago
• showteeth / ggcoverage
  Visualize and annotate genomic coverage with ggplot2
  ☆270Updated 11 months ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆327Updated 2 years ago
• xiaolei-lab / rMVP
  A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
  ☆317Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆351Updated 7 months ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆123Updated last year
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆173Updated this week
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆181Updated last month
• ANGSD / angsd
  Program for analysing NGS data.
  ☆250Updated 10 months ago
• YaoLab-Bioinfo / shinyCircos
  an R/shiny application for creation of Circos plot interactively
  ☆158Updated 3 years ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆117Updated 4 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆148Updated 10 years ago
• YongxinLiu / Metagenome
  Metagenome analysis pipeline
  ☆100Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆227Updated 5 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆218Updated 5 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆254Updated 5 months ago
• TongZhou2017 / itol.toolkit
  Helper Functions for Interactive Tree Of Life (iTOL)
  ☆179Updated 2 months ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆272Updated 3 months ago
• cxli233 / SimpleTidy_GeneCoEx
  A simple gene co-expression analyses workflow powered by tidyverse and graph analyses
  ☆212Updated 4 months ago
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆190Updated 2 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆301Updated 3 months ago
• knausb / vcfR
  Tools to work with variant call format files
  ☆265Updated 2 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆243Updated 4 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆288Updated 3 weeks ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆210Updated last year
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆229Updated 5 months ago
• wwood / kingfisher-download
  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
  ☆287Updated 4 months ago