The bottom line is that you should always test profile mixture models amongst the set of models you are testing and check in the log file that they were actually tested. I recommend always trying C60+G, since any deeptime data set will usually find that model to fit best (probably with ELM or EAL)
Very important work!
Pisani, @elpiratavell.bsky.social et al. dissipate doubts about the utility of models accounting for compositional heterogeneity across sites and identify CAT-GTR as one of the most flexible models in the phylogenomic arsenal.
🔗 doi.org/10.1093/molbev/msag090
#evobio #molbio #phylogenomics
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
New #ISEPpapers by @deemteam.bsky.social! Reversal to osmotrophy in eukaryotes www.nature.com/articles/s41...
"Distant eukaryotic lineages convergently reverted from predation to osmotrophy through co-option of bacterial genes and their mobilization via eukaryote-to-eukaryote HGT"
#Protists
I'm reposting this because I want to make a correction. In the thread below I mention using the -mset flag for testing site profile mixture models. But in fact you should use -madd flag. I'm sorry for this mistake.
I should say that I think -mset will work, however, the way I said it would in that thread. See this discussion thread on the IQ-TREE discussion group: github.com/orgs/iqtree/...
Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu
🎄 Just published 🎉! Our ongoing genome sequencing of the basal dinoflagellate Oxyrrhis marina uncovered a new lineage of endogenized Polinton-like viruses, OmPLV. Notably, OmPLV encodes ... [cont]
#VirEvol #MicroSky #Mevosky #SymbioSky #ProtistsOnSky
