Hello, everyone! I'm going to calculate the genetic distance between individuals for microsatellite data. Many previous studies that I know did this analysis by using MICROSAT software, but it appeared that all links they listed to this software have failed to direct to the right address. I have no idea what the problem is. Could anyone please share me a valid link or the software or any good suggestion for doing this analysis? Many thanks in advance.
Information about the MICROSAT software as follows:
Minch E., Ruiz-Linares A., Goldstein D., Feldman M., Cavalli-Sforza L.L. (1996) Microsat (version 1.5): a computer program for calculating various statistics on microsatellite allele data.
http://lotka.stanford.edu/micorsat/microsat.html
http://lotka.stanford.edu/microsat.microsat.html
http://lotka.stanford.edu/research/distance.html
http://lotka.stanford.edu/microsat.html
http://hpgl.stanford.edu/projects/microsat/
Dear Fang
I can not help you with the MICROSAT link, but indeed you can find several excellent softwares you can use to analyze your SSR data. Among them, ARLEQUIN, GENALEX, SPAGEDI, R libraries MMOD, POPGENREPORT, HIERFSTAT, etc.
This should keep you going
Dear Pablo,
Thank you very much for your answer. I have tried GENALEX and AELEQUIN before, but, as far as I know, the former can only handle the data with less than 1000 individuals (mine is more than it), and for the latter it seems that there is not a proper algorithm for calculating genetic distance between individuals, or in other words, I can’t find a proper option do this analysis (Intra-population level methods), as there is only one population in my data.
I am trying to analyze it using the rest of the software that you recommended, and hope they can deal with my data. Once again, thank you very much for your prompt answer. I really appreciate your help. :)
Best regards
Fang Wang
I would probably recommend that you start looking for R packages, one package I use a lot is PopGenReport, although Im not sure what the max amount of individuals is for that package. However, with PGR you have a choice of genetic distances between individuals. There are loads of packages that you could potentially look at ex. 'adegenet' (not sure if this last one calculates inter-individual distances though).
Hi Fang
You're welcome. I'm not sure how many individuals Spagedi can handle, but one of its beauties is the large amount of inter-individual distances it provides.
Dear Jimena
Thank you very much for your great suggestion. I tried PopGenReport package today as you mentioned. It’s really a great program for population genetic analysis and can calculate at least two kinds of genetic distance between individuals. Its way presenting the results is attractive and I really like it, but unfortunately, my data is still too large to its computing power. PopGenReport should be a good choice if my data has less individuals. Thanks you for sharing this with me.
Best wishes
Fang Wang
Dear Fang Wang,
You can use the Darwin program (http://darwin.cirad.fr/). I use it to calculate individual distance. It has a graphical interface easy to use. In addition to producing good dendrograms and statistics related to its representativeness.
I also have MicroSat if you want I can send to you. You can also use the MSTOOLS, however it will not make the distance, but rather the identity using the same algorithm that is used in MicroSat.
I have helped. If I can not have other way to calculate, but harder because we will need to use different programs.
I'd recommend MS analyzer
http://onlinelibrary.wiley.com/doi/10.1046/j.1471-8286.2003.00351.x/abstract
easy to use and as far as I know can handle very large datasets. seems the website (http://i122server.vu-wien.ac.at/MSA/MSA_download.html) is down but it was working 3 days ago so you can see a cached copy in google.
I recommend populations software too, it can handle relative large data sets and compute a large number of distances....
Most of the common software packages were indicated in the first three replies, but you could include NTSYS and some packages in R.
Dear Ivandilson Pessoa Pinto de Menezes,
Thank you very much for your answer! DARwin does have a good interface and is a great tool for analysis relevant to tree construction. It seems that it provided a new idea to define (dissimilarity index) the genetic distance which has inspired me. Many thanks to you！
For the Microsat software, if it is convenient could you please send me one? (My email: [email protected] ) Thank you in advance. I didn’t try the MSTOOLS, for I was unable to download it, but you mentioned that it was similar to the Microsat. :)
Best regards
Fang Wang
Hello, Mark
Thank you very much for your considerate answer. I know MSA before, but I almost forget it. I performed the analysis yesterday and got the same result to Population software’s (Md-Sajedul Islam and Gregoire recommended). What’s more, MSA was a little faster than populations when implemented the same analysis. Thank you!
Best regards
Fang Wang
Hello, Danny
Thank you very much for your answer. You are right. I think most of the relevant softwares have been recommended by the former replies and each has its advantages and restrictions [According to my experiences only: GENALEX (less than 1000 individuals, SPAGEDI (slow for large data size), R package mmod (dist.codom, remove all individuals with NAs for global estimate), R package PopGenReport (data size should smaller than 71.2Mb), Darwin program (using dissimilarity represent genetic distance), populations software, MSA analyzer(a little faster than populations when dealing with large data set) ]. I benefit a lot from all the answers.
Thank you very much for your NTSYS recommendation though I failed to be able to download it. I know one more good software now. Thank you!
Best regards
Fang Wang
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