🚨 Introducing NovelTree: A Nextflow workflow for highly parallelized phylogenomic inference! 🚨. Pub:.GitHub (software):.GitHub (analysis code & walkthrough):. @ArcadiaScience.A 🧵, 1/8

RT @DawidZyla: I worked on a small project this weekend that bridges learning with usefulness. As mentioned in my earlier tweet, bioRxiv ho….

RT @phylogenomics: Job opportunity for evolutionary biologists:.

RT @ArcadiaScience: ⏩ “That is what we think will be the key for our startups — we want to find the shortcuts through evolution”. @seemayc….

RT @jgschraiber: We updated this preprint based on a bunch of awesome comments we got from too many people to name, and think it's become a….

RT @PracheeAC: 🚨New @ArcadiaScience job alert!.We’re looking to add an evolutionary biologist to our platform team to help us develop metho….

🚨Heads up all computational evolutionary biologists - we've got an awesome new job opening at @ArcadiaScience just for you!🚨. Join me in building our our platform capabilities to screen the tree of life, accelerating our basic and translational research!.

If you want to talk more about this and are at #TAGC24, come by my poster - P921 - tomorrow, Saturday 3/9 at 8:00 PM!.

And of course, a big thanks to all contributors to this recent work - @PracheeAC, @thecrispress, @jasminebneal, and @ryanayork!.

We can’t wait to hear from you! These questions are not exhaustive — but still, they're quite extensive! Your feedback will be invaluable for us to triage our efforts so that we can focus on the research directions that will benefit the community. 6/6

C. How can we best extend NovelTree to become a truly “whole-genome” phylogenomic method?. Like other similar methods, NovelTree is restricted to proteins. How can we use whole-genome data (e.g., leveraging synteny) to conduct phylogenomics on the rest of the genome?. 5/6.

B. How can we scalably implement protein structural phylogenomics?. With the rapidly growing availability and clear utility of protein structural predictions in phylogenomic inference, now is the perfect time to think meaningfully about how to integrate the two approaches. 4/6.

Broadly speaking, we’d love to hear your thoughts on a few key questions…. A. How can we improve our gene family inferences (e.g. w/o using protein annots)?. Given the downstream importance of gene family inference, we want this step to be as rock-solid as possible!. 3/6.

Since publishing NovelTree last year (, we’ve been hard at work improving the method, focusing on improving its stability and computational efficiency. However, we’ve also been brainstorming about how we can extend it, making it capable of even more!. 2/6

Calling all evolutionary biologists and phylogenomics buffs! In our recent Open Questions pub, we ask for your thoughts on how we might improve and extend NovelTree, our workflow for scalable phylogenomic inference. Read and reply!. 1/6.

RT @ArcadiaScience: Are you attending #TAGC24 and interested in comparative phylogenomics methods?. Chat with @AustinHPatton on Sat 3/9 abo….

RT @lpachter: It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation….

RT @biorxiv_evobio: Tree sequences as a general-purpose tool for population genetic inference #biorxiv_evobio.

RT @jgschraiber: I'm excited to share this new preperint with @mwpen and @DocEdge85 about the unifying mapping approaches within and betwee….

RT @PracheeAC: Good at thinking through high leverage research projects that you’re happy to iterate on or sunset if they don’t pan out so….