Genomics for Aotearoa New Zealand

A simple and efficient software to perform PCA and Clustering analysis For population VCF File.

A tool for species tree - gene tree inference and reconciliation.

R tools for Population Genetics Tutorial by Grünwald et al

Tools for filtering SNP data sets derived from RADseq or Genotyping-by-Sequencing methods.

NCBI BLAST+ finds regions of local similarity between sequences.

ossutil allows you to efficiently manage objects in Object Storage Service (OSS).

Plink2: Whole genome data analysis toolset.

Stacks is a software pipeline for building loci from short-read sequences.

ape: Analyses of Phylogenetics and Evolution

Poppr: R package for analysis of populations with mixed modes of sexual and clonal reproduction.

vcfR: Manipulate and Visualize VCF Data

hierfstat: Estimation and Tests of Hierarchical F-Statistics

dartRverse An accessible genetic analysis platform for conservation, ecology and agriculture

SNPrelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

tess3r - Tool for analyzing population genomic data

LEA: An R package for landscape and ecological association studies

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

Toolkit for manipulating BAM (genome alignment) files.

SAMtools is a set of utilities for interacting with and post-processing DNA sequence read alignments

SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Syncs files to cloud storage.

Process Variant Call Format files

DNA sequence read aligner.

BCFtools is a program for variant calling and manipulating VCF and BCF files.

DiscoSnp++ and DiscoSnpRad

GFANZ container for the software polyRAD

DNA sequence read aligner.

Atropos is tool for specific, sensitive, and speedy trimming of NGS reads.

Sequence quality stats and visualisation of second-gen sequencing data.

Trimmomatic is a sequence read trimming tool for Illumina technology.