I'm hiring a postdoc (start date flexible) and a PhD student (for Fall 2027) to work in any area of computational phylogenetics! More info here:

mhibbins.github.io

I will be attending both PEQG and Evolution in June, so please reach out if you want to chat at these meetings!

I'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! Computational lab. Message me if interested, and can apply here: indiana.peopleadmin.com/postings/32547

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

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.

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.

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.

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.

PhyloLens - Visual Studio Marketplace Extension 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...

Efficient 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

@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

📣 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 - harvardinformatics/snakemake-executor-plugin-cannon: A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster - harvardinformatics/snakemake-executor-plugin-cannon

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...

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

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...

Photo of an aye-aye

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/...

Aronoff Lab at The Ohio State University

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

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!

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!

Hmm, yea that could work. I wonder if there is any mouse data that could work for this? @jeffreygood.bsky.social
Although, I'm not sure how to map shortbreads. Maybe some batches with BWA-kery? :D

Yea that would definitely help pinpoint which SNPs are being miscalled. I was also hoping to dig into why they are being miscalled - mis-mapped reads? unmapped reads? something else? Which I can't think of how to do without a truth set for the mappings themselves.

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

GitHub - goodest-goodlab/pseudo-it: Beta version of the new pseudo-it software for iterative reference guided assemblies. Beta version of the new pseudo-it software for iterative reference guided assemblies. - goodest-goodlab/pseudo-it

We've (@jeffreygood.bsky.social) implemented this in pseudo-it (github.com/goodest-good...), though hard to quantify the effects without good simulations, which I've yet to find the right read simulation program for. Ideally want simulated bam and vcf to compare mapping and SNP calls. Ideas welcome!

Great to work with @ekopania.bsky.social, @jeffreygood.bsky.social, and everyone else on this project! I was happy to be able to present Emily's cool figure showing dN/dS of genes in different tissues and different time-points at Evolution a couple years ago:

Geometriphylogenetics

I'd like to see the alignments...

xkcd.com/3010

oh hey I wrote a FAQ for this question www.molecularecologist.com/2024/08/13/f...

For phun I made a "starter pack" for people involved in developing phylogenetic methods. If you feel you should not be involved, or feel I missed you (it is difficult!), please let me know. go.bsky.app/D7LsGUM 🧪

Multiple, Tenured/Tenure-Track Faculty Positions in Computing in Biology, Health, and Wellness - Bloomington, Indiana job with Indiana University Bloomington | 664327 Invite applications for multiple tenure /tenure-track positions at the Assistant, Associate, or Full Professor ranks

🚨🚨🚨Jobs at IU!🚨🚨🚨
Multiple positions in computational biology, broadly interpreted. Positions can be in multiple depts, including Biology, Informatics, and CS.

Please apply--we want new colleagues!

jobs.sciencecareers.org/job/664327/m...

I'm recruiting students / postdocs to join my new lab at the University of Rochester for Fall 2025 onwards! If you're interested in phylogenetic comparative methods, genome evolution, and/or computational biology, please get in touch! More info:

mhibbins.github.io

A table with the title "Concordance factors for branch ID 545". It shows a table with 4 columns (concordance and discordance factors) and 3 rows (gene, site, and quartet). Each cell contains a percentage representing the proportion of the genes, sites, or quartets which match a particular tree. Cells with higher numbers are coloured darker red.

A phylogeny showing six major clades of birds. Next to each is a table of concordance vectors.

For phylo nerds interested in concordance and discordance...

Here's a tutorial that helps you calculate gene, site, and quartet concordance vectors for any branch on your tree.

iqtree.org/doc/recipes/...

(work with @3rdreviewer.bsky.social)

#phylogenetics 🧪 #evolution

Adam Freedman gives a great overview of the pros and cons of current genome annotation pipelines. If you have RNAseq data, use BRAKER or Stringtie, if you have a high quality closely related annotation, TOGA performs very well. #Evol2024

New preprint with Rob Lanfear!

"The meaning and measure of concordance factors in phylogenomics"

ecoevorxiv.org/repository/v...