TraitLab: a Matlab package for fitting and simulating binary tree-like data

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dc.contributor.authorKelly, Luke J.
dc.contributor.authorNicholls, Geoff K.
dc.contributor.authorRyder, Robin J.
dc.contributor.authorWelch, David
dc.date.accessioned2026-03-03T16:50:03Z
dc.date.available2026-03-03T16:50:03Z
dc.date.issued2023-08-17
dc.description.abstractManual describing the TraitLab software for phylogenetic inference. TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits are simultaneously lost while new ones arise, and borrowing, whereby traits transfer laterally between species as well as through ancestral relationships. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distribution for tree topologies, clade and root ages, and the trait loss, catastrophe and borrowing rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for heterogeneity in the trait loss rate, biases in the data collection process and borrowing of traits between lineages. Coupled pairs of Markov chains can be used to diagnose MCMC mixing and convergence and to debias MCMC estimators. The raw data, MCMC run output, and model fit can be inspected using a number of useful graphical and analytical tools provided within the package or imported into other popular analysis programs. TraitLab is freely available and runs within the Matlab computing environment with its Statistics and Machine Learning toolbox, no other additional toolboxes are required.en
dc.description.versionpreprint
dc.format.extent37
dc.format.mimetypeapplication/pdfen
dc.identifier.authororcidKelly, Luke J.§0000-0003-4653-9303
dc.identifier.authororcidNicholls, Geoff K.
dc.identifier.authororcidRyder, Robin J.
dc.identifier.authororcidWelch, David
dc.identifier.citationKelly, L J, Nicholls, G K, Ryder, R J & Welch, D 2023 'TraitLab: a Matlab package for fitting and simulating binary tree-like data' arXiv, pp. 1-37.
dc.identifier.endpage37
dc.identifier.otherArXiv: http://arxiv.org/abs/2308.09060v1
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/18594
dc.language.isoen
dc.publisherarXiv
dc.rights© 2023, the Authors.
dc.rights.accessrightsopen access
dc.subjectstat.CO
dc.subjectBayesian inference
dc.subjectDollo model
dc.subjectDating methods
dc.subjectMarkov chain Monte Carlo
dc.subjectPhylogenetics
dc.subjectBinary data
dc.subjectTrait data
dc.subjectHistorical linguistics
dc.subject[Maths]
dc.subjectManual describing the TraitLab software for phylogenetic inference
dc.titleTraitLab: a Matlab package for fitting and simulating binary tree-like dataen
dc.typeArticle (preprint)
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