Supplemental Code: Hiscott et al (2016)
Here is a copy of all MATLAB code used to conduct simulations and analyses for:
Hiscott, G., Fox, C. Parry, M. and Bryant, D. Efficient recycled
algorithms for quantitative trait models on phylogenies.
http://arxiv.org/abs/1512.00890
SplitsTree4
I am a co-author of SplitsTree4.0, with Daniel Huson. SplitsTree is a fairly hefty application for constructing phylogenetic networks of many sorts. Anyone using Neighbor-Net should use the implementation in SplitsTree as it is the fastest and most carefully debugged.
For downloads and manual, see the SplitsTree site at www.splitstree.org
PopART
I worked with Jessica Leigh on PopART, a powerful and user-friendly software package for the construction, display, and analysis of haploytype networks.
For downloads and manual, see the PopART site at popart.otago.ac.nz
SNAPP
I am a co-author of SNAPP, which is efficient software for inferring species trees and species demographics from largescale SNP or AFLP data (or indeed, any unlinked, binary markers). The software resulted from a colloboration with Remco Bouckaert (Auckland), Joe Felsenstein (UWash), Noah Rosenberg (Stanford) and Arindam RoyChoudhury (Columbia).
| Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N., RoyChoudhury, A. 2012 Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 19(8):1917-1932 |  |
For downloads and manual, see the SNAPP site at http://www.beast2.org/snapp/
MCMC simulation software:
This software implements an MCMC framework for running simulation experiments, as described here. Please contact Jessica Leigh if you download it. The domestication code is my implementation of the model described in Allaby et al (2008). mcmctools is a Python module for running MCMC-based simulations as described in our manuscript.
DistR
DistR estimates relative evolutionary rates of different genes by comparing distance estimates. The method is described in
| Bevan, R., Franz Lang, B. and Bryant, D. 2005. Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis. Systematic Biology 54(6):900-915. pdf |
The software and documentation can be downloaded here:
Rachel Bevan has also produced a version of PhyML that handles multiple gene rates. We have shown that this produces significantly improved phylogeny estimates. You can download it from the PhyML website.
Phi test
The Phi Test is a simple, rapid, and statistically efficient test for recombination. Its performance is comparable with coalescent based methods like LDHat, and yet it can be applied to large alignments with hundreds of sequences. The test, and extensive experimental assessments, can be found in
| Bruen, T., Phillipe, H. and Bryant, D. 2006. A quick and robust statistical test to detect the presence of recombination. Genetics 172, 2665--2681. pdf |
The software and documentation can be downloaded here:
The test is also available as part of SplitsTree4.
Other software packages
- PAUP I worked with Dave Swofford to code the least squares and maximum agreement subtree algorithms currently implemented in PAUP.
