Home

FrogCap Phylogenomics

Welcome to the FrogCap sequence capture tutorial section! Here you will find tutorials using the github scripts to process your target enrichment data from the raw reads to constructing phylogenetic trees and filtering for SNPs.

Tutorials

Tutorial 0: Customized FrogCap probeset

Tutorial 1: Cluster and program setup

Tutorial 2: Data preprocessing (cleaning raw reads, decontamination, assembly)

Tutorial 3: Data alignment (target marker matching, alignment, alignment filtering)

Tutorial 4: Tree estimation (gene trees, concatenation, species trees) COMING SOON

Troubleshooting: random issues that arise