Software by
David Posada
MODELTEST (MAC-WIN-UNIX) - estimates the model of DNA
substitution that fits the data best among 56 models. It performs
maximum likelihood ratio tests and calculates their associated
P-values to test several evolutionary hypotheses. Also
calculates AIC values. Compatible with PAUP*4 beta 3 and
later.
TCS (MAC-WIN) NEW (et alli) - implements estimation of the TCS
network (as described by Templeton et al. 1992, Genetics
132:619-633) from DNA sequences, or nucleotide distances. Also
estimates other parameters, as the 95% parsimony limits and
outgroup weights.
GEODIS (MAC-WIN) - implements the nested clade
analysis (NCA) of the geographical distribution of haplotypes
developed by Alan Templeton et al. This methodology partitions
population processes from population patterns.
COLLAPSE (MAC) - is a program for collapsing sequences to
haplotypes. The program indicates which sequences are collapsed
to which. At the same time generates a file with the haplotypes
in PHYLIP format. Gaps can be treated as a fifth state.
If you download any
of these programs, and want to be informed about potential bugs
or updates, please send an e-mail to dposada@uvigo.es
Additional Software
TreeSAAP
The program Tree SAAP measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.
MatrixGen
The program MatrixGen allows researchers to generate protein scoring
matrices based on their own aligned data sets. These matrices can then
be used by an alignment program to generate a more accurate alignment.
Felsenstein's
Software Page
Last Updated: August 18, 2004
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