Thanks for the reply. May I know can this software be linked with Arlequin to directly map the results?

I'm afraid you'll have to make the map by yourself. It's rather easy using for instance QGis, which is free to use.

Thanks for your reply. Can QGis be used with molecular data?

 Hi, Vindhya Mohindra,

My name is FangFang, come from Chinese Academy of Sciences, Beijing, China. Sorry to disturb you. I am writing to ask you for help with running the software of SAMOVA2.0.

 I have read the information in the web of the software (http://cmpg.unibe.ch/software/samova2/#Introduction), but I don’t know how to run the soft, especially the details of every step. When I have three files including test.sar, test.geo, and test.arp, I double clicking on SAMOVA2_console.exe, then should I input the three files step by step? The web doesn’t tell us how to use this program in details. Would you please to help me for this? Many thanks!

FangFang

Fang, you should enter input file  name without extension, in your case you should type "test", press enter and follow samova questions.

Dear Researchers,

I have a question about initial configuration of groups to try parameter. What it means and what value should be entered ? Unfortunately, this information is not specified at the website of the software.

Thank You in advance.

Marcin Kuciński, I set number of initial configuration of groups = 100.

On the SAMOVA website there are some information in the algorithm section: "To make sure that the final configuration of the K groups is not affected by a given initial configuration, the simulated annealing process is repeated 100 times, starting each time from a different initial partition of the n samples into the K groups".  I understand this as a recommendation to set 100 initial configurations.

http://cmpg.unibe.ch/software/samova2/

Dear Yulia,

Thank You for your response. You are right. At the first time, I have understood the cited by You information as the simulated annealing process is repeated 100 times (default value) to make sure that the output configuration of the K is not affected by entered value of initial configuration. I have checked manually what is happening in the algoritm when different values of initial configuration are entering. Like You said a given value of initial configuration of groups parameter determines the number of repeats during the simulated annealing process.

Best regards

Hi, Vindhya Mohindra,

Sorry to bother you.My name is Li Ke, a graduate student from China Agricultural University, I want to ask you for help with running SAMOVA2.0.

It always display “No vertex found for a bisector…hit any key” when I running the program. I guess there are something wrong with my inputfile.  I have compared with the templates. Unfortunately,I did not find any problems. what's more, my inputfile are operating normally in Arlequin. I have no idea what causes this issue. Would you please give me some advice?

Thank you for your time.

Ke Li

Hi, Vindhya Mohindra,

Can I consult that why the SAMOVA 2 software stops working when I try to run it? I put the two files in the same directory with the software. The question of the data format can exclude, for that the example given also failed. Can you give me some suggestion? Looking forward to your reply. Thank you.

Best wishes,

Ping

hi every one in the group,

just a bit of help...as mentioned in the previous conversation by ke  li.......

 i was trying SAMOVA from few days,  i am getting the similar  display “No vertex found for a bisector…hit any key” when I running the program.

I wanted to know if any one has got a solution to the problem. 

thank you

For “No vertex found for a bisector…hit any key”， just hit any key and the program will end after incomplete running. and open the file "SAMOVA2" generated in the same directory and check the problems in the end of the file.

 Thank you sir. 

Sorry, I want to ask a question

How to interpret the SAMOVA analysis output?

Thank you

i have sequence and geographic data, i want to do analysis using SAMOVA 1.0

can anyone help how to provide an example data input format to the application?

because I have a little difficulty in compiling the data formula.

thank you

winda

Thank you very much for the explanation and examples of data compilation formats, it really helped me in working on research data.