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2brad_denovo

Genome-wide de novo genotyping with 2bRAD

2brad_utilities

A collection of scripts for analyzing 2bRAD genotyping data.

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

apoptosis_data_pipeline

This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.

beast2

Bayesian Evolutionary Analysis by Sampling Trees

beast2_constsites

Update your BEAST2 XML to account for constant sites

bedops

:microscope: BEDOPS: high-performance genomic feature operations

belize_mcav_symbiodiniaceae_its2

Symbiodinium spp. DNA extraction & amplification protocols and bioinformatic pipelines

bigdataanalysis19

bio594_2019

URI - EVOLUTIONARY AND ECOLOGICAL GENOMICS (BIO 594)

bio_594_2019

Repository for BIO 594 Spring 2019

biocluster

Tutorial on building a computing cluster for bioinformatics

biocore_documentation

Central repo for all non-project-specific documentation. Includes biocore best practices and guidelines.

cubamcavmsatsnp

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

ddocent

a bash pipeline for RAD sequencing

dsuite

Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

genomics_general

General tools for genomic analyses.

gghybrid

R package for analysis of hybrids and hybrid zones

gomez-corrales-prada_mol_eco_2020

Code and files needed to reproduce analyses in the associated publication (10.1111/mec.15631,https://doi.org/10.5061/dryad.9kd51c5f3)

ipyrad

Interactive assembly and analysis of RAD-seq data sets

islands-paper

Detect "islands of speciation" in nightingale genome. This is the analysis part of the paper.

lcwgs-guide-tutorial

matiasgoco.github.io

Notebook of a PhD student in Prada`s Lab

nested-sampling

Nested sampling packagin for BEAST

ngstools

Programs to analyse NGS data for population genetics purposes

ostrea_popstructure

This repository contains code and notebooks detailing preliminary analyses of Genotype-by-Sequencing (GBS) data in the Olympia oyster (Ostrea lurida).

papers

phrynomics

A collection of R code for dealing with SNP data and analyses

physalia-lcwgs

Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 19-22 2020