Custom scripts for estimation of retention/loss patterns of the rho-derived duplicates.
Taikui Zhang, PhD (Department of Biology, the Eberly College of Science, the Pennsylvania State University)
For the user on Mac with the arm64 CPU architecture, please find scripts in the folder named Scripts_For_Mac_arm64. In addition, we also provided a test version on the mac with the x86_64 CPU architecture (see scripts in the folder named Scripts_For_Mac_x86_64) and an online tool available in capsule (https://codeocean.com/capsule/2265752/tree/v1).
Generally, our scripts comprise four steps (functions) as described below. Step1, removal of long branches in gene trees; Step2, rooting gene trees; Step3, estimating retention/loss patterns; and Step4, filter by gene pairs mapped at the nodes earlier than Poaceae.
These scripts can be applied specifically on the phylogenomic analyses of our tree datasets on FigShare and the small test dataset provided here.