Can anyone suggest a population genetic analysis software?

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When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

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i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Sean M Hoban Popular answer

I agree with Per, you need to be more specific. However, for general analysis, Genepop is a classic, as is GDA (Genetic Data Analysis) and FSTAT. In R, you can use some of these: http://cran.r-project.org/web/views/Genetics.html In addition, for a comprehensive overview of population genetic analysis software, the review of Excoffier and Heckel is still pretty good even though it is nearly 8 years old. http://www.nature.com/nrg/journal/v7/n10/full/nrg1904.html

There are many other lists of genetic analysis software on the internet including the following links:

http://www.discat.unipi.it/BiolMar/utilities/progs.htm

http://biology.duke.edu/noorlab/software.htm

http://softlinks.amnh.org/microsatellites.html

http://evolution.genetics.washington.edu/phylip/software.html

http://courses.washington.edu/fish543/Software.htm

Per Kryger

GenAlex is a good place to start, but your question is not very precise, what type of analysis and which kind of data?

Sean M Hoban

Abdul-Latiff M.A.B

Thanks for the response guys! I'm using mitochondrial DNA data.. I'm trying to evaluate the genetic structure of the population, population expansion, gene flow, inbreeding, population viability etc2..

You got a long list above to search from. I believe a question like inbreeding you can not answer with mtDNA, since it is only inherited maternally. Before you rush to the software, you need to study the manuals and papers attached, to see if indeed your data and your question fits the tool.

Thank u very much :)

Ferruccio Maltagliati

Dear Abdul, at the beginning of my reasearch career there were only a couple of programmes for population genetics analysis. Now there are dozens... You can find a list of them at the following web site: http://evolution.genetics.washington.edu/phylip/software.html. I am not sure that the list is complete.

Thanks Mr Ferruccio! appreciate the help!