Dear Ali,

You may also try the software Alleles In Space (AIS):

http://alleles-in-space.software.informer.com/1.0/

Good luck,

Temim

Dear Ali, 

Besides GeneAlex, Genodive also performs Mantel Test. In addtion, there are different R packages available to perform Mantel Test. One convenient package to get genetic diversity estimates and to perform Mantel Test  is PopGenReport 

https://cran.r-project.org/web/packages/PopGenReport/PopGenReport.pdf

and landgenreport performs Least-Cost- path modelling analysis

https://cran.r-project.org/web/packages/PopGenReport/vignettes/Tutorial_landgenreport.pdf

Best, 

Cristina

Thanks so much all of you is really help me!

You can do a Mantel test in GenAlEx, but you could also try Arlequin, Genepop (on the web) has IBD, maybe FSTAT. Alternatively, there is a program called IBD.

Thanks Sam

Dear Ali,

You can find one method in the paper "IBD (Isolation by Distance): A Program for Analyses of Isolation by Distance". You can also try "http://ibdws.sdsu.edu/~ibdws/distances.html". I also suggest to try "http://biodiversityinformatics.amnh.org/open_source/gdmg/" for geographic distance calculation. 

Best,

Jie

Dear Jie,

Thanks so much for really helpful software!  

http://ibdws.sdsu.edu/~ibdws/

That online program is not only user-friendly, it can also be used to for partial mantel test 

Good luck

Thanks so much Magdalene!

Hi Ali Kareem

What method did you end up using for IBD please? I've been looking for IBDWS but it doesnt seem to be working anymore.

Hope all is well,

Simone

I do not know the online software, but you could carry out it easily with Genalex or some software in R. Hope this is useful.

Cheers,

Jie

Hi Simone,

There are a couple of IBD methods that can be carried out in R, since you are savvy with that. Alternatively, there are other programs such as GenAlEx, which i know you are already familiar with and SPAGeDi (http://ebe.ulb.ac.be/ebe/SPAGeDi.html). I am pretty sure that Ali used GenAlEx (because i helped him with it). Hope the papers are coming together well.

Hi Simone

Hope you doing well, as Sammy mentioned I used GenAlEx for IBD and it is fine

Thanks Sammy and Ali- I will try GenAlEx again - getting weird errors with SPAGeDi even though I am following the manual. Hope you are both well!

Hi Ali,

I think, the Isolation by Distance Web Service (IBDWS) 3.15 will be useful for the analysis of Mantel test of matrix to test the significance of relationship.

I hope that the following papers will give some idea for your analysis.

1. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. Bmc Genetics, 6, 13.

2. Ridley et al. (2011) The spatiotemporal dynamics of T. castaneum adult flight and gene flow. Molecular Ecology 20: 1635 - 1646.

You can use GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA. sequences. I hope this could help you.

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