#4 · Genomics

Probabilistic tools for phylogenetic ESS, species trees, alignment windows, and dating

The common thread is explicit probabilistic modeling used to infer evolutionary parameters from genomic data. Preprints address Bayesian tree effective sample size via CCD-based emulated MCMC chains with new ESS estimators, STEQ as a statistically consistent quartet-distance species tree method under the multispecies coalescent, and PhyloNOW, which extends window selection to variable sizes for whole-genome alignments. The published item, phyloHessian, integrates phylogenetic Hessian matrices into PAML-MCMCtree to enable mixture-model molecular dating, applied to ancient symbionts. What is new is the inferential machinery packaged as usable software. These items are method and tool descriptions rather than shared benchmarks, so no comparative performance claims are made across them.