Phylodynamics software

Software
1

A list of software packages for phylodynamic analyses.

To add:

  • TreeDater
  • others?
2

BEAST

The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.

Features:

  • Time trees
  • Population size dynamics
  • Evolutionary rate estimation
  • Phylogeography models
  • Epidemiological models
  • Ancestral state reconstruction
  • Synonymous/non-synonymous rate estimation

http://beast.community/

Citation: Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Suchard, Lemey, Baele, Ayres, Drummond & Rambaut (2018) Virus Evolution, 4: vey016, Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 | Virus Evolution | Oxford Academic Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 | Virus Evolution | Oxford Academic

3

BEAST2

http://beast2.org/

4

TempEst

TempEst (formerly known as ‘Path-O-Gen’) is a tool for investigating the temporal signal and ‘clocklikeness’ of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is designed for analysing trees that have not been inferred under a molecular-clock assumption to see how valid this assumption may be. It can also root the tree at the position that is likely to be the most compatible with the assumption of the molecular clock.

  • Citation
    A. Rambaut, T. T. Lam, L. M. Carvalho and O. G. Pybus (2016) Exploring the temporal structure of heterochronous sequences using TempEst. Virus Evolution 2(1): vew007. DOI: http://dx.doi.org/10.1093/ve/vew007

http://beast.community/tempest

5

TreeTime

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

  • Citation
    Sagulenko P, Puller V, Neher RA. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution. 2018;4(1):vex042. doi:10.1093/ve/vex042.
6

LSD

The LSD software includes very fast dating algorithms, based on a Gaussian model closely related to the Langley–Fitch molecular-clock model. This model is robust to uncorrelated violations of the molecular clock. The algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint).

  • Citation
    Thu-Hien To, Matthieu Jung, Samantha Lycett, Olivier Gascuel; Fast Dating Using Least-Squares Criteria and Algorithms, Systematic Biology, Volume 65, Issue 1, 1 January 2016, Pages 82–97, https://doi.org/10.1093/sysbio/syv068

http://www.atgc-montpellier.fr/LSD/