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

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!

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...

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/...

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!

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:

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 🧪

🚨🚨🚨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

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...