This website might give you some initial lights:

http://methodspopgen.com/

Also, note it has a arXiv paper associated to it.

Danny: for what purpose (association to phenotype/genetic distance/forensic/etc?)

how many of them (tens/thousands/millions?). cheers alessio

Conservation genetics, so distribution of genetic variation for the first round. Then I have geo-references points to do some fine scale spatial genetics work. I am using about 120 to 150 SNP markers for these studies.

Structure (Pritchard http://pritch.bsd.uchicago.edu/software.html) is used by thousands of scientists for population genetics and works very well with SNP. You can do individual assignement to populations, admixture etc. In his web you may find other useful software. For geographic association you may google "Mantel test". Or use the "see what you compute" Genalex software which runs on top of Excel (http://biology.anu.edu.au/GenAlEx/Welcome.html). You may also see the researchgate page of Stephane Joost (https://www.researchgate.net/profile/Stephane_Joost/) who has done a lot on "landscape genomics". cheers alessio

Hello Alessio,

I have had experience with Structure and it is a useful program. I am fairly well versed in multivariate statistics and spatial genetic stats, so I can work with the SNP data. I just recently downloaded the GenAlEx packages and see real promise. I like being able to actually have more of a user interaction when running stats (not point and click), but I do need to upgrade my Excel version (2007 is buggy according to the authors). Thank you for the Stephane Joost lead. Sincerely, Danny

I would recomment the abilities of the adegenet package http://adegenet.r-forge.r-project.org/

Very versatile functions, population structure, plotting and also incorporation of spatial data.

Have fun...

Thanks Tobias. I have been having pretty good luck with GenAlEx, which I have found very helpful with data format issues for many different programs. As the spring goes on, I look forward to exploring some of the possibilities with GenAlEx and Adegenet. Thanks, Danny

You may consult this work

http://onlinelibrary.wiley.com/doi/10.1111/biom.12004/abstract

Thank you Novonil. I will look into this software. Danny

Hi Danny you can also use GenALEX for SNPs data. It is really useful.

Thanks Demir,

  That is what I have been using and it does offer a lot of flexibility. Danny

for some reason I can't get it to work on my computer.

can you suggest a way to operate it ?

Try to work with Genalex it is very easy. You just need an excel with all the complements    Good luck

I have used GenAlEx for much of the population genetic and spatial genetic SNP, SSR, and ISSR datasets I am working with - since my original posting. Structure is also another approach. I am blessed with typically working with polyploid species and I looked into the PolyR software - solid program and reasonable approach with challenging species. It does, however, not work with polygenic inheritance - tetraploid species with some markers that show tetraploid and some showing diploid inheritance. I hope this update helps.

I want to construct Phylogenetic tree for SNP data. I want to know which software is latest to use for this SNP.

USE Mega X

PLINK software is almost universal for processing SNP data.

thank you

This website might give you some initial lights:

http://methodspopgen.com/

Also, note it has a arXiv paper associated to it.

thanks for this. it is useful.