Gregg Thomas

marketplace.visualstudio.comPhyloLens - Visual Studio MarketplaceExtension for Visual Studio Code - View phylogenetic trees in VS Code (Newick, NEXUS, PhyloXML, NeXML).

Blizzard outside, so I'll post about my first foray into fully agentic AI coding. I picked something I'd been wanting to do for a while, but had no experience with prior: a VSCode extension to view phylogenies in the editor. The result is PhyloLens. marketplace.visualstudio.com/items?itemNa...

At times I would ask for suggestions, which the chatbot of course would provide. A surprising number were useful, leading to feature creep in what was supposed to be a very simple app. Though in the end I'm happy where it ended up. Now working on updates for better performance for huge trees.

github.comGitHub - gwct/PhyloLens: Simple phylogenetic tree viewer extension for VSCodeSimple phylogenetic tree viewer extension for VSCode - gwct/PhyloLens

BY FAR the most time was spent tweaking the UI. It is still not great at that, though surprisingly I found that providing screenshots does seem to help. We'll see how this (or any AI code) holds up as I have to maintain it. Feel free to leave issues/ideas on the repo. github.com/gwct/PhyloLens

marketplace.visualstudio.comPhyloLens - Visual Studio MarketplaceExtension for Visual Studio Code - View phylogenetic trees in VS Code (Newick, NEXUS, PhyloXML, NeXML).

I hope the extension will be useful, and it already has been for me, but it does leave me with thoughts on agentic coding. I'd guess overall time spent was about 6-8 hours of actual "work" chatting with the agent, which is not a lot of time for full project development.

But I started with a very simple design: an extension to VIEW phylogenies. It accomplished this almost immediately, but I was also able to see the potential for more (editing, conversion, image export) once I had that in place.

marketplace.visualstudio.comPhyloLens - Visual Studio MarketplaceExtension for Visual Studio Code - View phylogenetic trees in VS Code (Newick, NEXUS, PhyloXML, NeXML).

Molecular Biology and Evolution

The interface provides status badges for the tree to tell you whether its rooted, binary, ultrametric, and allows for some minor editing and conversion between text formats as well as image export, though I don't see this as being useful for pretty tree pictures.

Gregg Thomas reposted

@molbioevol.bsky.social

15 Dec 2025

@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST). 🔗 doi.org/10.1093/molbev/msaf282 #evobio #molbio #compbio

doi.orgEfficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)Abstract. The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversi

Gregg Thomas reposted

Fábio K. Mendes

@fabiology.bsky.social

12 July 2025

📣 The Mendes Lab is recruiting PhD students in statistical phylogenetics! Interested, or know someone who might be? Details here 👉 tinyurl.com/542wyfb9 — please share!

github.comGitHub - harvardinformatics/cactus-snakemake: Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clustersSnakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters - harvardinformatics/cactus-snakemake

4 June 2025

Recently I developed several Snakemake workflows for tasks related to Cactus and HAL files, including whole genome alignment and pangenome inference. The goal was to perform these tasks efficiently on SLURM-based (or possibly other) clusters. I hope they are useful! github.com/harvardinfor...

informatics.fas.harvard.eduResources - Harvard FAS Informatics Group

4 June 2025

Each task has an associated tutorial on our group's website: informatics.fas.harvard.edu/resources/#t... Feel free to reach out if you want to use any of these workflows and need help getting started or run into any issues!

github.comGitHub - harvardinformatics/snakemake-executor-plugin-cannon: A Snakemake executor plugin for submitting jobs to the Harvard Cannon clusterA Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster - harvardinformatics/snakemake-executor-plugin-cannon

4 June 2025

Relatedly, but for a narrower audience, I also adapted the Snakemake SLURM executor plugin to perform automatic partition selection on the Harvard Cannon cluster. I was surprised by the amount of flexibility the plugins allowed, which may have finally won me over to them. github.com/harvardinfor...

Gregg Thomas reposted

Matthew Hahn

@3rdreviewer.bsky.social

10 Feb 2025

New paper led by @glom.bsky.social! "Unprecedented female female bias in the aye-aye, a highly unusual lemur from Madagascar" 1/ journals.plos.org/plosbiology/...

Gregg Thomas reposted

James Pease

@jamesbpease.bsky.social

10 Jan 2025

The Pease Lab in the Dept of Evolution, Ecology, and Organismal Biology at The Ohio State University is looking for a Postdoc interested in genotype-phenotype-environment evolution in plant and animal genomes. Details at osu.wd1.myworkdayjobs.com/en-US/OSUCar... and more info at www.peaselab.org

Gregg Thomas reposted

Emily Moore

@ecmoore.bsky.social

9 Jan 2025

If you know anyone who might be interested in working as a technician before a PhD, I'm looking for someone to work with me to generate some amazing data to understand the genetics of behavior, sex differences, and reproduction in an evolutionary context. Bonus? Amazing and supportive department!

Gregg Thomas reposted

Emily Kopania

@ekopania.bsky.social

7 Jan 2025

Our paper on the evolution of male reproduction in murine rodents was selected as the editor's choice article in the January issue of Evolution!

Evolution@journal-evo.bsky.social

This month's #EditorsChoice article: "Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents" by Kopania et al. @ekopania.bsky.social https://buff.ly/3PoYFSE

4 Dec 2024

A thorough look at what I think is an often overlooked problem in popgen and comparative genomics in general!

Jazlyn Mooney@jazlynmooney.bsky.social

First major paper from the lab! The work was led by super talented postdoc Maria Akopyan. She explored how reference bias skews estimates of diversity, demography, divergence & recombination rate with help from @elliecat.bsky.social & awesome ungrad Matthew. Full thread coming soon 🤓