Doyle, J.J., 1995. The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative. Systematic Botany, 20(4), pp.574–588.
Available at: http://europepmc.org/abstract/AGR/IND20522043.
Maximum Likelihood Analysen
- Goldman, Jon P. Anderson, Allen G., N. (2000). Likelihood-Based Tests of Topologies in Phylogenetics. Systematic Biology, 49(4), 652–670. http://doi.org/10.1080/106351500750049752
- PAML (for Phylogenetic Analysis by Maximum Likelihood)
- Comparison and tests of phylogenetic trees
- Estimation of parameters in sophisticated substitution models, including models of variable rates among sites and models for combined analysis of multiple genes or site partitions
- Likelihood ratio tests of hypotheses through comparison of implemented models
- Estimation of divergence times under global and local clock models
- Likelihood (Empirical Bayes) reconstruction of ancestral sequences using nucleotide, amino acid and codon models
- Generation of datasets of nucleotide, codon, and amino acid sequence by Monte Carlo
- Estimation of synonymous and nonsynonymous substitution rates and detection of positive
selection in protein-coding DNA sequences
- Bayesian estimation of species divergence times incorporating uncertainties in fossil calibration
- Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
- Publication: Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8), 1586–91. http://doi.org/10.1093/molbev/msm088
BEAST - Bayesian Evolutionary Analysis Sampling Trees
Description: "BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results."
Drummond, A.J. et al., 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular biology and evolution, 29(8), pp.1969–73.
Available at: http://mbe.oxfordjournals.org/content/29/8/1969.
MrBayes - Bayesian Inference of Phylogeny
Description: "MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters."
Ronquist, F. et al., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology, 61(3), pp.539–42.
Available at: http://sysbio.oxfordjournals.org/content/61/3/539.
- Splits Tree
- Homepage: http://www.splitstree.org/
- Publication: Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23(2), 254–67. http://doi.org/10.1093/molbev/msj030
- SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.