Alternatives and similar repositories for GAPIT

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

• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆202Updated last year
• BGI-shenzhen / LDBlockShow
  LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
  ☆202Updated 7 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 4 months ago
• TickingClock1992 / RIdeogram
  ☆191Updated 5 years ago
• showteeth / ggcoverage
  Visualize and annotate genomic coverage with ggplot2
  ☆271Updated last year
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆191Updated 3 months ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆125Updated last year
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆180Updated last week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• TongZhou2017 / itol.toolkit
  Helper Functions for Interactive Tree Of Life (iTOL)
  ☆182Updated 3 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆232Updated 7 months ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆252Updated 11 months ago
• taowenmicro / ggClusterNet
  Microbial ecological network visualization clustering
  ☆144Updated 2 months ago
• cxli233 / SimpleTidy_GeneCoEx
  A simple gene co-expression analyses workflow powered by tidyverse and graph analyses
  ☆213Updated 5 months ago
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆356Updated 8 months ago
• YongxinLiu / Note
  ☆125Updated 4 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆149Updated 10 years ago
• YongxinLiu / Metagenome
  Metagenome analysis pipeline
  ☆100Updated 4 years ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆276Updated 4 months ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆119Updated 4 years ago
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆393Updated 2 years ago
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆193Updated 3 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆245Updated 5 years ago
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆233Updated last week
• YongxinLiu / EasyMicrobiome
  ☆145Updated last month
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆183Updated 2 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆340Updated 10 months ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆386Updated 11 months ago
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆215Updated 7 months ago