Phyling

Aug 7, 2025 · 1 min read
projects

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample’s protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs.

workflow

If you’re interested in Phyling, please refer to the GitHub page for more details.

Phylogenomics Python Workflow
Cheng-Hung Tsai
Authors
Cheng-Hung Tsai (he/him)
I am a Bioinformatician with a PhD from UC Riverside (Dr. Jason Stajich Lab), specializing in the intersection of software development and large-scale genomics. My work focuses on building efficient UNIX/Python tools for genomics and metagenomics applications. I bring a unique perspective to the dry lab, having spent my early career at the bench mastering protein purification and molecular biology. I am passionate about creating user-friendly, scalable tools that empower researchers to turn raw sequencing data into biological discovery.