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TraitLab: A MatLab package for fitting and simulating binary tree-like data

By Geoff K. Nicholls, Robin J. Ryder and David Welch

Abstract

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 “catastrophes”, evolutionary events where many traits are simultaneously lost while new ones arise. The core of the package is a Markov chain Monte Carlo sampling algorithm that enables the user to sample from the Bayesian joint posterior distributions for tree topologies, clade and root ages, and the trait loss and catastrophe 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 borrowing (horizontal transfer) of traits, heterogeneity in the trait loss rate and biases in the data collection process. Both the raw data and the output of MCMC runs can be inspected using a number of useful graphical and analytical tools provided within the package. TraitLab is freely available and runs within the Matlab computing environment.

Year: 2013
OAI identifier: oai:CiteSeerX.psu:10.1.1.363.6709
Provided by: CiteSeerX
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