I am carrying out an experiment to look at the genetic diversity of individuals from this endangered plant species endemic to Madagascar (Xerosicyos tripartitus). We don't know if these individuals come from the same population. All we know is that they are from the same plant species. So in other words this is an intraspecific study of genetic diversity. I have amplified DNA at 3 different regions(trnE-trnF, trnS-trnG and trnC-petN1R).I am about to send the purified DNA samples to a company for sequencing. So my results are DNA sequences at 3 different regions. Can any of you recommend a program that I could use to in order to analyse the results I would get?
Hello Paolo, try with TCS from David Posada's Lab. It produces a haplotype network of closely related sub-species: http://darwin.uvigo.es/our-software/
Or, you try with any other program that gives you an information about genetic distance: http://evolution.genetics.washington.edu/phylip/software.html
good luck!
carolina
We use CLC workbench for our intrahost diversity analysis, think it is a pay for program though.
How about BLASTClust? It clusters together sequences based on the stringency parameters you set. By this you can detect all the different haplotypes you my have. You can use it from here: http://toolkit.tuebingen.mpg.de/blastclust
Dear Paolo,
You can try MEGA (www.megasoftware.net/) to align, edit and even analyse your sequences. In your case I would like to suggest the following softwares: Network (http://www.fluxus-engineering.com/sharenet.htm) and DNAsp (http://www.ub.edu/dnasp/).
All the best
Hello Paolo,
You could use PAUP. You need to have a license to use it, though. An open source software could be MEGA. However, PAUP allows you to change the settings and run different evolutionary models. Other option would be to use a Bayesian software such as MrBayes.
Regards,
Cinthya
Hi Paolo,
Normally we study the genetic diversity by looking into the haplotypes as well as their grouping through Median-joining network. Like what had been suggested by Paiva, DNAsp is a great software to generate data files for haplotypes and Median-joining analyses using NETWORK.
Also, Arlequin (http://cmpg.unibe.ch/software/arlequin35/) can help you to get their FST values to compare the nucleotide diversity and AMOVA to conclude whether they're genetically structured or not. You can use FST value to discuss the gene flow.
You should also try STRUCTURE (http://pritch.bsd.uchicago.edu/structure.html) to look into their population structures.
Following are some articles that might be useful for you:
Lim, H. C., Lim, P. T., Su, S. N. P., Teng, S. T. & Leaw, C. P. 2012. Genetic diversity of Pseudo-nitzschia brasiliana (Bacillariophyceae) from Malaysia. Journal of Applied Phycology 24(6):1465-1475.
http://link.springer.com/article/10.1007/s10811-012-9803-7
Silvia Casabianca, Antonella Penna, Elena Pecchioli, Antoni Jordi, Gotzon Basterretxea, and Cristiano Vernesi
Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea
Proc R Soc B 2012 279: 129-138.
http://rspb.royalsocietypublishing.org/content/279/1726/129.full.pdf+html
Cheers,
HongChang
Thank you for all your suggestions. Eventually the consensus sequences showed no SNPs. We did not need to do any analysis of genetic diversity, as indeed the genetic diversity was virtually none. So we just concluded that that was due to inbreeding.
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