Comparative Methods Topics and Links
Continuous Character Analysis
download a new program from the Ackerly lab at Stanford (see Ackerly, D. D. and M. J. Donoghue. American Naturalist. 152). Macintosh format
Biogeographic Analyses and Coevolution
Rates of Evolutionary Change
Spot (Sequence Parameters Of Trees) by Andrew Rambaut and Nick Grassly of the Department of Zoology, University of Oxford. SPOT is a program that will calculate the likelihood of a given tree topology for a set of aligned nucleotide sequences. For each topology, SPOT will estimate the maximum likelihood values of branch lengths and other parameters of the model of nucleotide evolution that has been chosen. Such parameters include the ratio of transitions to transversions (TS/TV ratio) and relative rates of substitution at different codon positions. Branch lengths can also be constrained to assume a molecular clock hypothesis. Multiple datasets and multiple trees can be analysed which is useful for performing MonteCarlo simulations of hypothesis (parametric bootstraps). Although SPOT does not estimate tree topology, an accompanying program, SPOTSHELL, will iterate between fastDNAml and SPOT until the maximum likelihood parameters and topology has been found (or at least something close to it).
Sources of Homoplasy
Bi-De Andrew Rambaut of the Department of Zoology, University of Oxford has written Bi-De, to simulate the evolution of trees using various models of lineage birth and death, and sampling lineages from among those extant. It can simulate branching with or without regulation of the number of lineages. It also allows the user to specify the relationship between the number of lineages and the birth rate of lineages.
Seq-Gen (Sequence Generator) Andrew Rambaut and Nick Grassly of the Department of Zoology, University of Oxford, a program that will simulate the evolution of nucleotide sequences along a phylogeny or multiple phylogenies, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. The models available are the Hasegawa, Kishino and Yano (HKY) model, the Felsenstein F84 model, the general reversible model, the Kimura 2-parameter model and the Jukes-Cantor model. Rate heterogeneity among sites or among the different positions within a codon can be specified.
PSeq-Gen (Protein-Sequence Generator)version 1.0 Nick Grassly and Andrew Rambaut of the Department of Zoology, University of Oxford, PSeq-Gen , which will simulate the evolution of protein sequences along evolutionary trees. Three common models of amino acid substitution are implemented (PAM, JTT, and mREV), allow for user-defined amino acid frequencies. Site-specific rate heterogeneity following a gamma distribution is allowed. The program can handle multiple trees and produce multiple data sets.
Estimating Divergence Times
QDate version 1.1. Andrew Rambaut of the Department of Zoology, University of Oxford. QDate estimates the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known. It analyzes the data under three models: (1) a perfectly clocklike model, (2) a model in which one pair has a different rate of divergence than the other, and (3) a model in which all branches have different rates. The method is described in the paper: Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442-
by John Huelsenbeck is a program that tests the consistency of a tree with
stratigraphy of the species. It uses a permutation test described inthe
paper Huelsenbeck, J. 1994. Measuring and testing the fit of the stratigraphic
record to phylogenetic trees. Paleobiology 20: 470-483.
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