Yep, I don't buy the idea that the species tree is a good proxy for the ground truth for a given (short) domain alignment. But then I usually care more about branch lengths and other parameters than topology.
Now out in G3: academic.oup.com/g3journal/ad... (thanks to the editors and reviewers for attention to detail and efficiency!)
@jessthorpemas.bsky.social (I'm mainly a magpie)
I got my E-M1 Mkii and 300mm f4 certified refurbished (they're both 7 years old now). I often bring the 40-150 f2.8 (bought second-hand) and 1.4x TC on bike rides, and then regret not having taken a longer lens.
I'm not sure "jealous" is the word I'd use, they seem a bit messy :) bmcgenomics.biomedcentral.com/articles/10....
Background Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morpholo...
…and there are widgets to filter, query, and extract sequences for downstream analysis. For code and more examples, see: github.com/CobiontID/re...
VAE-based framework to explore long-read datasets and identify potential contaminants or cobionts - CobiontID/read_VAE
Given compositional differences, sequences from different sources form distinct clusters in the VAE’s latent space. For example, the pictured moth (blue) is infected with Wolbachia (red). No labels? Discrepancies in coverage and coding density (second image) often provide clues.
Have long-read data and want to know what you've really sequenced, and how much of it? Reliable taxonomic labels are often scarce if the target is from a less well-explored group. Fortunately, 2D embeddings from a VAE can tease apart different organisms in read sets: www.biorxiv.org/content/10.1...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Disentangling Cobionts and Contamination in Long-Read Genomic Data using Sequence Composition www.biorxiv.org/content/10.1101/2024.05.30.596622v1
The recent acceleration in genome sequencing targeting previously unexplored parts of the tree of li
My last half-used can went in a jar in the freezer (I don't like it in desserts, but it's allowed in asian and caribbean dishes).