Haplogroup Classification at Scale
How yallHap works, and what I learned building a Y-chromosome haplogroup caller that doesn't choke on 185K SNPs or ancient DNA.
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About
Hi! My name is Alaina, and I'm a Canadian data scientist who taught herself molecular and computational biology starting in 2011. I spend a lot of my free time doing bioinformatics—population genetics, ancient DNA, that sort of thing.
This is where I share what I'm working on and the tools I build along the way. The "X" in xbio doesn't mean anything specific. (Exponential biology? The X chromosome? The unknown variable? Pick your favourite.)
I work in AI and health science, but the stuff on this site is just me chasing haplogroups through time because I think it's interesting. And also because I think that I can bring 35+ years of software engineering to make science more reproducible and accessible.
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Explorations
Write-ups of what I'm working on. Mostly population genetics and ancient DNA stuff.
Making Haplogroup Callers Work with Ancient DNA
Ancient DNA is a mess—damage, low coverage, missing data. Here's how I think about building classifiers that can handle it.
Exploring the Growth of mtDNA Diversity
Are "extinct" lineages actually extinct, or just undersampled? Hunting for missing branches in the mitochondrial tree.
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Tools
Open source tools for genomics research. First-class support for ancient DNA, but tastes great with modern DNA too.
yallHap
Y-chromosome haplogroup classifier
An ancient-DNA-friendly Y haplogroup caller using the YFull tree with 185K SNPs. Features Bayesian scoring designed specifically for aDNA damage patterns, achieving 99.9% accuracy on modern samples and 90.7% on ancient DNA.
View on GitHubeveHap
Mitochondrial haplogroup classifier
Coming soon—mtDNA classification using similar probabilistic approaches optimized for ancient samples.