This is a beta version of yvyra. The core MCMC engine and diagnostic
tools are functional, and MCMC results are cross-validated against
upstream MrBayes 3.2.7a after each change to the source code (deterministic
match under identical seeds and settings). Still, the software has not
been validated extensively enough for use in published studies, and
results should be treated as preliminary.
Several features from the roadmap are not yet integrated, including
ancestral state constraints (root priors), continuous traits, estimated
transition rates, and temporal calibration for clock trees. These are
planned for upcoming releases.
If you are interested in using yvyra for your work, or would like to
collaborate on its development, I would be glad to hear from you.
Contact: Tiago Tresoldi
(tiago.tresoldi@lingfil.uu.se).
Changelog — 0.2.0
Rooted clock trees (new default). YAML analyses now use a
rooted birth-death tree with an IGR relaxed clock. The root is inferred by
the model, so no outgroup is needed. Set tree_model: unrooted
for the old behavior. Choose a clock model with
clock: strict|igr|iln|tk02|cpp|wn.
Fix rooting artifact for unrooted trees. In unrooted mode,
the first taxon was silently pinned at the root. A dummy outgroup is now
injected and pruned from output. Thanks to Deepthi Gopal for reporting
this bug.
G U I D E
yvyra
Bayesian inference of phylogeny for linguistics and culture
yvyra (Guarani: "tree") adapts the Mk model framework (Lewis 2001) and
the MrBayes MCMC sampler (Ronquist et al. 2012) for historical linguistics,
stemmatology, and cultural phylogenetics, with asymmetric evolution models,
character weights, confidence-weighted tips, and per-character diagnostics.
Asymmetric modelsDirectional cost matrices: lenition is common, fortition is rare
Character weightsWeight characters by comparative importance
Confidence tipsEncode uncertainty in fragmentary attestations
Character diagnosticsWhich characters drive each clade
Sensitivity analysisTest robustness to individual character removal
Runs in your browserNo installation. Full engine compiled to WebAssembly