You can use the Popgene for genetic diversity and the Discriminant Analysis of Principal Component (DAPC) through the R package adegenet for population structure.

I think there is a wide variety of software for such purposes. I use commonly Arlequin, or DnaSP.

Regards,

Cristian

It depend also of your markers, your problematic and so on... for instance, if you have microsatellites there are some multitools software existing like GenAlEx or Genetix (in French). 

Hi Aript, 

    Review paper by Excoffier & Heckel will help you make a choice about softwares that best fit your data, your purpose, and your operation systems.  

Laurent Excoffier & Gerald Heckel

Computer programs for population genetics data analysis: a survival guide

Nature Reviews Genetics 7, 745-758 (October 2006) | doi:10.1038/nrg1904

http://www.nature.com/nrg/journal/v7/n10/abs/nrg1904.html

Hi,

i refer you to this adress because It depend also of your markers, your problematic....

 http://tomato.biol.trinity.edu/programs/index.php/Category:Program

http://fsffrance.org/science/biologie.fr.html

http://www.appliedbiosystems.com/absite/us/en/home/support/software-community/free-ab-software.html (spicific for SNP softwar)

http://turing.une.edu.au/~agbu-admin/BESSiE/

this is sadly a thorny path we all should go through... probably the best approach is to see in which situation your data fit in: Excoffier, L., & Heckel, G. (2006). Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics, 7(10), 745-758.    http://www.nature.com/nrg/journal/v7/n10/abs/nrg1904.html

It depends on your markers, for microsatellites:

- For population structure you can use Structure which works together with structure harvester. 

- For genetic diversity, you can use Arlequin.

- To transform any of your files use create

Estimation of the various parameters of genetic diversity can be estimated using GENETIX (4.03) and FSTAT (2.9.3.2) software. We can estimate the observed heterozygosity (H0), the expected heterozygosity (HE), the total genetic diversity (HT), the genetic diversity within populations (HS), the genetic diversity among populations (DST= HT-HS) and the coefficient of gene differentiation (GST= DST / HS) (Nei, 1987). Wright’s fixation indices (FIS, FST et FIT) (Weir and Cockerhamm 1984), partitions the genetic diversity within a species by estimating: the fixation of alleles in all populations (FIT) and in subpopulations (FIS), and genetic differentiation among subpopulations (FST).

The isolation by distance among populations can be estimated through the Mantel procedure implemented in GenAlex (Peakall and Smouse 2012).

Genetic differentiation between each pair of populations can be estimated using Genepop 4.0 (Rousset 2008).

For genetic diversity and population structure analysis the best available software's are POPTREE, POPGENE, ARLEQUIN, STRUCTURE, and R Software packages. They can fulfill all your queries and needs.

As mentioned above the software tool to analyze genetic diversity and population structure will depend on the question and on the marker/s used. GenAlex can be used for a variety of markers and can estimate both diversity and structure (AMOVA), and you can also use it to translate your data into other programs infile. For example Genepop, DnaSp, Structure, Fstat. To add another point of view Migrate and DIYABC, can be used to estimate migration rates and effective population size using Bayesian statistics.  

From my experience,STRUCTURE + ARLEQUIN use to work quite well.

hello,

for fine-scale spatial genetic structure, SPAGEDI (OJ Hardy and X Vekemans), is also very nice (and of friendly use).

best regards

Hi Arpit,

Fstat and Spagedi are good programs for analysis Intra and inter-population. With Spagedi you can do analysis of genetic structure and draw conclusions about collecting seeds in the case of breeding or conservation programs (> 100 samples/individuals inside the population).

all the best

Hi Arpit,

For population structure analysis you can use STRUCTURE, TESS, GENELAND, and DAPC. All of these programs use different approaches but worth testing. Good luck!

Moumita Sinha Hello I used poptree for the matrix and the tree but I couldn't get the p value. how could I have it

Genalex is very nice if you don't have too many samples, but being based in Excel means very large numbers of SNPs may be too many for Excel to handle and/or the processing takes forever. (I had problems with 12,923 SNPs) Too bad...it was/is a nice application.

AlphaEase4C, Power Marker, NTSYS-PC

After sequencing of the specific region from different populations of insects the sequences were edited and aligned using software like Bioedit and CLUSTAL. The aligned file of sequences can be used for construction of phylogenetic studies by using distance matrices, maximum parsimony method, neighbour joining, branch-and-bound parsimony method, bootstrapping with the help of programmes like MEGA7, PAUP, PHYLIP. The softwares like DnaSP are very useful for haplotype diversity analysis. The evolutionary and geographical relationships among haplotypes, a median-joining (MJ) haplotype network was constructed with Propart software. The neutrality tests like Fu and Li’s D_test and F_test and Tajima’s D tests and genetic differentiation help for finding demographic history information can be performed using DnaSP software for detecting the range of population expansions. The software’s like Arlequin and DnaSP are used to know pairwise genetic distance (FST) calculate the genetic variation between and within different populations

I have analyzed 16000 SNPs with GenALEx. You can try it. You have to set the data for it.

Best wishes

Abdullah

Hello

For population structure analysis you can follow Plink based "ADMIXTURE".

https://dalexander.github.io/admixture/

You can also use STRUCTURE software

https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html

For diversity analysis you can try Power marker or NTSYS-PC

RKGanapati