Dear all,
For studying the genetic diversity of the species within and between its populations, microsatellite or SSR markers is used in different groups of a multiplex. For bin setting and data analysis of the geneMapper report, what is the available software can be used?
with all the best,
Dadamouny
Dear Mohamed
السلام علیک
For AMOVA analysis by SSRmarkers, Popgen and GenALEx are appropriate and efficient to study interpopulatin diversity and intrapopulation diversity and for genetic diversity, mentioned software and Power-marker and NTsys are suitable...
Dear Mohamed
For bin setting, I use the R library MicrosatAllele. It is not updated, so it doesn't appear in the CRAN repository of actual packages, but you can download it from http://alberto-lab.blogspot.com.es/p/code.html and make a local install into R. Other software for binning alleles: Flexibin, Allelobin, Tandem, etc.
Regarding software for the analyses, the two previous answers name several good programs. I could add ARLEQUIN and, in case you are intereded in the new genetic differentiation measures that originated after Jost (2008) paper: "why Gst relatives do not measure genetic differentiation", the R library mmod..
Dear Pablo G. Goicoechea
Do you have R package for genetic diversity of SSR?
Dear all, thanks for your valuable answers!
Sorry Dr. Atefeh Sabouri! Unfortunately, I haven't that package. For the moment, R is not easy for me to use it (as it has a lot of commands), so I asked on direct easy software for analysis the population genetics. If R package is recommended, may I try. Thanks for considering and your interest!
All the best!
Mohamed
Dear Mohamed
Thanks for your response. However I asked Pablo for R package and I remember you looking for a easier software.
Best Regards
Atefeh
Dear Atefeh
You can download the packages from the CRAN repository. Once you are within R, write the following commands:
install.packages("mmod", dep=T)
install.packages("PopGenReñport", dep=T)
etc. And when you want to use them
library (mmod)
etc.
Please let me know if this was what you asked for.
Pablo
Dear Pablo
Thank you so much! Can I have your email adress if possible?
Best Regards.
Here it is:
work: [email protected]
home: [email protected] your answer
I just realized there is a mistake in my previous answer. The second install.packages line should read:
install.packages("PopGenReport", dep=T)
Cheers
Pablo
Dear Mohamed,
For bin setting in GeneMapper; this can be done within GeneMapper software. You can use Allelobin to corretly size your base scores. But you will need information on the repeat mottifs for the Primers.
Once you get the output in Excell; all the suggested softwares by previous contribotors could be used.
Best wishses.
Bramwel
Dear Mohamed
There are several softwares to use, as STRUCTURE for population structure analysis, genepop, FSTAT and popgene for basic statistics, and also GeneAlex for ANOVA or PCoA analysis, also a excel add-in called MStools will help you to transfer your original data into input format for several softwares. Tassel also could be used for building trees and doing some correlated analysis.
Good luck.
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