Data and code from: A colorful legacy of hybridization in wood-warblers includes frequent sharing of carotenoid genes among species and genera

Introgression between species has the potential to shape evolutionary trajectories in important ways, but uncovering complex introgression dynamics has only recently been made possible by advances in genomics. Warblers of the avian family Parulidae exemplify rapid diversification and sexual trait divergence, and we endeavored to study historical introgression in the family. We sequenced multiple genomes of nearly every species, constructed a phylogeny for the family, and investigated gene flow across the genome and at genes known for controlling feather color. The dataset and code presented here and in GenBank are intended for reproduction of all analyses, including processing reads, making the phylogeny, and several methods for investigating gene flow at various genes and in 10-kb windows across the genome., , # Data and code from: A colorful legacy of hybridization in wood-warblers includes frequent sharing of carotenoid genes among species and genera

Dataset DOI: [10.5061/dryad.1zcrjdg3v](10.5061/dryad.1zcrjdg3v)

## Description of the data and file structure

The dataset consists of a main folder, data-and-code.zip

### Process-data

#### Data

* bam-locations.example.txt - Example of a file to feed into merge-species-bams.sh to merge individual sample bam files into species bam files.

- align-rate.txt - Read alignment rate output from bowtie log files compiled in one place. Used to make Fig. S8.

#### Code

* trim-align-mark-index.sh - Code that takes demultiplexed raw reads and a reference genome, then trims adapters, aligns to the reference, marks duplicates, and indexes the resulting bam file.

- merge-species-bams.sh - Code that merges individual sample bam files into species bam files.

* call-variants.sh - Code that makes a (very large) unfiltered VCF file of SNPs, indels, and inv...,