Analysis (DISABLED - will be removed on 12/22/17)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/22/17. If you need this software, please contact help@msi.umn.edu.

 

The analysis toolset is C++ software for evolutionary genetic analysis.

Verision 0.8.4 is installed.

The set of tools installed on the HPC clusters are:

rsq : to summarize linkage disequilibrium in data
compute : a "mini-DNAsp" for the Unix command-line
kimura80 : o calculate divergence using Kimura's (1980) method 
gestimator : Ka/Ks by Comeron's method
polydNdS : to analyze silent and replacement polymorphism
HBKpermute : a program to perform the permutation tests for population substructure described by Hudson, Boos, and Kaplan  (1992)  Mol.  Biol. Evol. 9:138-151. 
MKtest : to perform McDonald and Kreitman tests
sharedPoly : a program to calculate number of shared polymorphisms between 2 partitions of an alignmentdescPoly : a program to output a qualitative summary of features of sequence polymorphism data 

 

 

Please see http://molpopgen.org/software/lseqsoftware.html for more specific information about these tools.

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