Using targeted sequence capture to identify evolutionary relationships among poplars and willows

This repository contains the scripts and analysis notebooks used for the creation of a novel genotyping platform that I designed, and its implementation reported in my paper Targeted sequence capture array for phylogenetics and population genomics in the Salicaceae, published in the journal Applications in Plant Sciences in 2020.

Contents

1. README.md: this file

2. notebooks/: Notebooks that detail the analyses reported in the manuscript in Jupyter Notebook format

3. probes/: The sequence of probes used for target capture, as well as a target reference file used by HybPiper for gene sequence assembly

4. scripts/: Python scripts I wrote to design the sequence capture array, and to analyze the resulting data

The raw read data obtained through targeted sequence capture will be available at the NCBI short read archive after the manuscript has been accepted for publication.