A practical approach to Simulating Heterochronic Sequence Alignments

Objective: The use of tip dates in phylogenetic analysis is becoming ubiquitous due to the increased availability of sequence data isolated at different points in time, i.e. , heterochronous datasets. Such datasets permit to co-estimate the absolute time of evolutionary events, expanding the capabilities of phylogenetic analyses without the previous requirement of knowing mutation rates and/or dates of internal nodes in the phylogeny. Currently, there is no ready-to-use script in the literature that is capable of generating simulated heterochronous sequence datasets. The aim of our work is to facilitate the generation of simulated sequences collected at different time points that can be use in simulate-based bioinformatic studies and testing of new phylogenetic methods, therefore facilitating and motivating extensive teaching and hands-on practice of multiple state of the art phylogenetic analytical approaches. Results: : We have written a script for the generation of heterochronous sequence datasets that integrates functions of previously published R and Phyton packages, including the packages TreeSim (R) and pyvolve (Phyton). Our code allows to generate user-defined number of datasets ( replicates ) with the desired sequences evolving following a designated evolution model among a defined number of topologies with a defined pattern of temporal sampling. The code also enables both simple and complex simulations, by taking advantage of the full range of options available with each package integrated in the code script.