Molecular Biology Computer Programs

GENECONV (Statistical Tests for Detecting Gene Conversion) - Version 1.81      (Vs. 1.81 posted 8-29-2000)

Given an alignment of DNA or protein sequences, GENECONV finds the most likely candidates for aligned gene conversion events between pairs of sequences in the alignment, as well as the most likely candidates for a gene conversion events from outside of the alignment. Candidate events are ranked by multiple-comparison corrected P-values and listed in a spreadsheet-like output file.

Provisions can be made for mismatches with a mismatch penalty. As a program option, sequences near the endpoints of candidate events can also be listed. Searches can be restricted to within-group gene conversion events only, which leads to more powerful multiple comparison procedures.

PRFMLE (Estimate Selection and Mutation Rates from Aligned Sequence Data) - Version 1.2     
(Version 1.2 posted 9-14-2001)

Given an aligned sample of DNA sequences from a coding region in a random-mating population, PRFMLE estimates the equilibrium selection and mutation rates that have been acting on the coding region. Both rates are scaled by the effective population size. Selection is assumed to act independently on different coding positions and is unidirectional either for or against new mutants.

PRFMLE assumes that there has been sufficient recombination so that polymorphic sites can be assumed to be independent. That is, loose linkage between sites is assumed instead of tight linkage. This may be a reasonable assumption if polymorphisms are sparse.
Under these assumptions, a diffusion approximation can be derived for the sample configurations at those sites that are currently polymorphic. The analysis can be carried out for amino-acid polymorphic codon positions, for silent polymorphic codon positions, or for both. The rates for silent codon positions estimate codon bias under the assumption of no mutational bias.
The mutation rate that is inferred from amino-acid polymorphisms is generally less than the rate inferred from silent codon polymorphisms. This reflects the proportion of new amino-acid mutants that are strongly deleterious. (The diffusion approximation only sees weakly-selected polymorphisms.)

Send any email comments to sawyer@math.wustl.edu

Stanley Sawyer
Department of Mathematics
Washington University in St. Louis
St. Louis, Missouri 63130, USA

Web address:   http://www.math.wustl.edu/~sawyer
Email address:   sawyer@math.wustl.edu

Both programs are free for academic use.

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    Last modified November 27, 2006