I want to construct a NJ tree for my microsatellite data which should be supported with bootstrap values. I downloaded the software Populations 1.2.31. I did not find any manual for that so tried to deal with the short guidlines section in the software webpage but couldnt get any result. even I could not open the input into the software. Can sombody help me to get through this?
I do not know with the latest version but with version 1.2.28, you first choose your option like for instance "2) Compute population distances + tree", you then provide the name of your input file, then the software offer you different options including phylogenetic tree with bootstrap, then distance option, and then the kind of tree option, and finally the number of bootstraps ... quite simple...
Dear Gregoire,
thank you for your answering. However it didnot worked though I followed your instructions. I am unable to load the input file. I have attached a screen shot of the message it sends when I type my input file name in the console. Could you please have a look at that? my input file name is populations input which is in genepop format.
thanks a lot.
I would guess it is related to the format of your file. I remembered to use .gtx file (provided by genetix software). What did you used?
I used .txt file which I used as the input for the Genepop software. I will try with a .gtx file.
thanks a lot
Dear Gregoire,
I tried with the .gtx file and i could open it and give the commands. but when the analysis is going to start the program suddenly stopped working. this happened for all available versions of Populations software including 1.2.29, 1.2.30 and 1.2.32. I could not find the version 1.2.28 that you worked with. Could you send me the link or the executable file of that version if you still have it with you?
thanks a lot
I do not think this relates to the population version (I just checked with 1.2.32, and it works with my .gtx) but more to the format of your file. Can you show a screenshot?
yeah. I have attached a scrrenshot. And I attached my input file as well. Can you have look at that?
thanks a lot
Hello Dhanusha,
I used Populations many times and never have any problem. And when I had some problem, it was always due to a wrong format of an input file. I always used ".txt". I attached one of my input files, so you can check it. The problem with program crash is most probably due to bootstrap analysis and missing data present in your input file. In this case, the program crash as soon as it will reach row with missing data. The best thing you can do is removing individuals with missing data. Then it should run without problems.
The issue actually relates to the format of your data set...
As your genotypes are presented as 3x2 digit columns, in the very beginning of your file, alleles have also to be given as 3 digit number and not 2 (011 and 012 and so on instead of 11 and 12).
Dear Gregoire and Majesky,
As you both suggested I formatted the input file by removing the missing data rows and changing the 3 digit numbers into 2 digits but the progrm gets crashed in the middle of the bootstrap analysis. I think now the data file is OK since it could be used with no error when the bootstrap analysis is excluded. however I need to draw the dendrograms with bootstrap values.So can you suggest some more steps for me to follow if possible?
thanks a lot!
Yes, I saw the software crashing sometimes (unsure why), but repeating the process 2 or 3 times with 1000 bootstraps (I do not think you need more) allow to obtain the tree.
Hi,
this happend to me also (fail of the software during bootstrap analysis), but as Gregoire wrote, run it several times until it will finish bootstrap analysis. This worked for me. There is some bug, but I am not sure where.
Thanks a lot for all of you. finally I could run the software after many tries and get it done with my analysis. thank you everyone for your support. it was really helpful for me.
Dear Dhanusha
I wanna use Population to draw NJ tree by using SSR data, howerer I couldn't any packages for installing Populaion, could you share your Population to me ?
Hi! I can't open output file too view the tree. Can anybody help me?
Hi Elina Soloshenkova ,
You can use FigTree software to open your output file (saved in newick format [.nwk] ) to view your tree. There are some online tools as well such as ITOL (https://itol.embl.de) but you can edit your tree easily with FigTree.
- Badges
- Science method
- Similar topics
- Biological Science
- Ecology