P

phylogenetics

SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.

For details go to the wiki-page

Compute phylogenetic trees from distance matrix using BioNJ algorithm. It will produce Newick file and Weighted newick if needed. There is also a render using Equal-angle algorithm and SVG output for testing. It's preferred to use a JS render like 'phylotree.js' (demo of phylotree.js here http://phylotree.hyphy.org/).

R scripts used to investigate whether biases in the fossil record sampling rate through geological time can bias global Phanerozoic diversity histories reconstructed using the phylogenetic diversity estimation (PDE) method.

Code repository for: Khouri, Z., Gillung, J. P., & Kimsey, L. S. (2022). The evolutionary history of mammoth wasps (Hymenoptera: Scoliidae). BioRxiv.

Bendixsen et al. (in review) Python data (.p files) and scripts used for data analysis of high-throughput sequencing data. Data depicts the phylogenetic fitness landscape of the self-cleaving CPEB3 ribozyme.