Stars
mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
This repository contains 12S mitochondrial gene reference sets that can be used with the RDP Classifier to classify 12S metabarcode sequences from fish.
Script to assign taxonomy to ASVs by parsing blastn data
r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)
A Julia package for estimating phylogenetic networks from genomic data
Bayesian analysis of genomic sequence data under the multispecies coalescent model
Sharing code for papers at BIO genetics group
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.
Caculate the genetic distance of Dxy(like Fst) between the two populations form the vcf file .
GeneMiner2 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