Github Repository of Published Papers

1 Overview

This is a Gihub Repository for Published Papers. This includes Rmarkdown files documenting and annotating all the methods used in the respective papers.

2 Papers

2.1 Shakya, S.B., Edwards, S.V. & Sackton, T.B. Convergent evolution of noncoding elements associated with short tarsus length in birds. BMC Biol 23, 52 (2025). https://doi.org/10.1186/s12915-025-02156-4

The files for the relevant sections are listed below for the paper:

• Cactus alignment
• OU analysis
• Get Conserved Elements
• ATAC-seq analysis
• PhyloAcc analysis
• Selection analysis

2.2 Shakya, S.B. et al. Genomic Associations of Skeletal Shape Variation in Waterfowl Limbs

• Duck analysis

3 Workshops

3.1 Harvard, Aug 2024

• Genome alignments using ProgressiveCactus and running PhyloAcc: (Harvard, Aug 2024) link