Crandall Lab

Crandall Lab Computer Programs

 

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) - 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