ksil91

giscus

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stdpopsim

A library of standard population genetic models

MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)

dDocent

a bash pipeline for RAD sequencing

NGS-PrimerPlex

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

Anacapa

Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).

pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes

Reproducible-science-in-R

This site provides information on conducting reproducible science using the R language.

Tag-seq

3’ Tag RNA-seq pipeline (Work in progress)

clustOpt

Scripts for the optimization of RADseq clustering thresholds in population genetics

eigenMT

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants

EecSeq

Protocol for Expressed Exome Capture Sequencing

eDNAFlow

project_juvenile_geoduck_OA

This repository provides data and scripts to analyze the influence of ocean acidification on juvenile geoduck DNA methylation and phenotype.

ASH_Putnam_Lab_Notebook

Open Lab Notebook

pseudo-it

An approach that iteratively generates pseudoreferences, incorporating sample-specific variation and reducing mapping biases

ABFT_popgentrace

find_sex_loci

Find sex specific loci from genome-wide genetic markers.

Hybrid-zone-mov