Comparative Analyses of a Whole-genome Alignment of Antbirds (Thamnophilidae)

Work in progress.

G. A. Bravo (gustavo_bravo@fas.harvard.edu) & S. V. Edwards (sedwards@fas.harvard.edu). Harvard University.

This repository will broadly contain scripts used for the following analyses. As scripts are uploaded, these categories may change or be redefined.

1. Genome assembly (TBA)
2. Genome quality assessment (TBA)
3. Genome annotation (TBA)
4. Whole-genome alignment using Progressive Cactus (TBA)
5. Creation of track hubs for the USCS Genome Browser (TBA)
6. Detection of conserved regions in antbirds (TBA)
7. Analysis of acceleration of Conserved Non-Exonic Regions (CNEEs) using PhyloAcc
8. Analysis of protein-coding regions (TBA)