GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
03.03.2026 17:41 โ
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Large genome model: Open source AI trained on trillions of bases
System can identify genes, regulatory sequences, splice sites, and more.
Evo 2 is here, and the scale is wild. Itโs trained on nearly 9 trillion bases across all domains of life, picking out regulatory DNA and splice sites that often trip humans up. Itโs fully open-source and already identifying critical BRCA2 mutations with impressive accuracy.
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05.03.2026 16:34 โ
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A digital CAPTCHA verification window titled "Select all squares with PIPES" against a plain white background. The window contains a 3ร3 grid of numbered squares, mixing literal hardware, smoking pipes, and programming syntax.
These captchas just keep getting harder #rstats
05.03.2026 15:58 โ
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That's a good name for software:
MKado: a toolkit for McDonald-Kreitman tests of natural selection
www.biorxiv.org/content/10.6...
05.03.2026 09:31 โ
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Good morning โค๏ธ
05.03.2026 13:57 โ
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Population genomics using ancient DNA data
21th-25th September 2026
๐จ Registrations are now open for the 4th edition of the course Population Genomics Using Ancient DNA with @arunsethuraman.bsky.social & @cegamorim.bsky.social ๐งฌ
Learn to analyse aDNA data, from data QC to population structure & demographic inference.
www.physalia-courses.org/courses-work...
04.03.2026 16:44 โ
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I think Calvin doesnโt think my breakfast looks very appetizing - whereโs the tuna, human?!
04.03.2026 17:40 โ
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On the expansion and evolution of a masterโs project
Academics often lament that hardly any masterโs projects โ even the best ones โ get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tel...
Academics often lament that hardly any masterโs projects get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tell how one masterโs project was, through persistent teamwork, finally carried over the finish line: go.nature.com/4aKs7N3
04.03.2026 14:24 โ
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Pic from my tenure + NSF CAREER award celebration party back in 2023 at Jodyโs! โค๏ธ
04.03.2026 06:35 โ
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I miss my Hey Lab peeps, but more importantly, I miss collaborating on all this fun science. Congrats to Alex & @sarahtishkoff.bsky.social on this new paper! I remember discussing ghost introgression with them back in 2013/14. So happy to see it come to fruition. www.science.org/doi/10.1126/...
04.03.2026 06:35 โ
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The core-pivotal index: a geometry-first approach to academic impact
The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careersโ achievements. Such an index wo
@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever.
๐ doi.org/10.1093/molbev/msag026
#evobio #molbio
03.03.2026 13:00 โ
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Awww! Thank you - this just made my day! โค๏ธ Hail our beautiful spider bebes!
04.03.2026 05:09 โ
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We are very excited to share a new resource from our team: spatial subcellular proteome maps in plants! We developed an MS-based method that registers localizations of about 8000 proteins in Arabidopsis roots in a single experiment.
(1/9)
www.biorxiv.org/cgi/content/...
03.03.2026 06:53 โ
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The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome https://www.biorxiv.org/content/10.64898/2026.03.01.708907v1
03.03.2026 15:31 โ
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Detecting and Quantifying Networks of Biological Kinship via Exponential Family Random Graph Models
Abstract. Genetic relatedness between ancient humans can help to identify close and distant connections between groups and populations, uncovering signatur
Excited to share our study in GENETICS on exploring biological kinship in ancient DNA data sets (doi.org/10.1093/gene...).
Using ERGMs to find variables that correlate with relatedness, and applied to 6th-9th century Avar, we find evidence for female exogamy and the existence of an elite class.
03.03.2026 09:16 โ
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Was seed color in early crops really chosen for aesthetics?
White seeds evolved repeatedly-not because humans preferred them, but because losing pigmentation reduced seed dormancy. Ecology, not intention, may have driven domestication. www.biorxiv.org/content/10.6...
#PlantScience #Domestication
03.03.2026 08:23 โ
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TLDR? Here, lemme be your AI chatbot and summarize it for you. 1) Donโt, 2) Absolutely not, 3) Nope, 4) No no no, and 5) Go see your real physician.
03.03.2026 01:39 โ
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Researchers in the US might be having feelings about writing grants atm-I know I am!
We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal.
His advice is gold, and helpful regardless of funder. Pls RT!
02.03.2026 15:32 โ
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We have a new preprint! - "Ancient Pathogen Genomics in Africa โ Current Evidence and Future Directions"
A review of current evidence, challenges, and opportunities for studying past epidemics and hostโpathogen evolution using ancient DNA from African contexts.
www.preprints.org/manuscript/2...
02.03.2026 13:55 โ
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Had my folks send me some golden oldies for my upcoming keynote lecture. Hereโs my mom running a teacher workshop in the early 90s, and my dad presenting his carburetor innovations to then Indian Prime Minister, Rajiv Gandhi in the mid 80s. โค๏ธ
01.03.2026 17:17 โ
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rambaut/figtree
Automatically exported from code.google.com/p/figtree - rambaut/figtree
The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I donโt really like the look of.
28.02.2026 19:01 โ
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๐น๐น๐น๐น๐น
28.02.2026 17:11 โ
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Please make it stop. Ugh. This is worse than Googling symptoms.
28.02.2026 00:24 โ
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Stanford researchers help trace ancestry for African Americans
A group of Stanford researchers is offering a mathematical model to help link family connections up to 410 years ago.
Excited that our work was featured on the local (Bay Area) news for their Black History month series. Interview with Noah and clips from my interview with @dornsife.usc.edu and CGSI talk in the article below
www.nbcbayarea.com/discover-bla...
26.02.2026 22:44 โ
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