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Bayesian haplotype-based genetic polymorphism discovery and genotyping.
An R package for creating Q-Q and manhattan plots from GWAS results
Vignette and research project developed under the AES ERC Networking Grant Scheme and the GSA workshop support scheme.
Automated and distributed population genetic model inference from allele frequency spectra
A short R script to calculate the Reich-Patterson FST estimator (Reich et al. 2009) and bootstraps from a genlight object.
stackr: an R package to run stacks software pipeline
Caculate the genetic distance of Dxy(like Fst) between the two populations form the vcf file .
EasyMiner is an enhanced version of our previous developments Easy353 and GeneMiner
ORTHOSKIM allows in silico capture of targeted sequences in genomic or transcriptomic libraries.
Geneminer: a software for extracting phylogenetic markers from next generation sequencing data
Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics
A collection of file format converters to prepare input for several popular phylogenetic and population genetics software packages.
Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with…
General tools for genomic analyses.
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
An R function to compute Concordance Factors from SNP datasets
Tutorials on phylogenomic analyses for the ForBio Phylogenomics course
An R package to generate species range maps based on ecoregions and a user-friendly GBIF wrapper
A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.
Reduced Representation sequencing Organellar read Genotyper