Hi Branislav

have you checked this web to look for?:

https://courses.washington.edu/popgen/Software.htm

You can compute distances in a software (e.g Populations) and then use the pairwise matrix in another (e.g Figtree)

Hi

I use Powermarker (http://statgen.ncsu.edu/powermarker/) to generate distance matrices and then view them in any number of programs (eg, MEGA, Splitstree)

Populations is a very simple program to do that:

http://bioinformatics.org/~tryphon/populations/

Paup is a good software for this purpose.

Phylip also works well, you can use it to create the desired distance matrix and then you can construct a number of different kinds of dendrograms. The infile is tricky, I recommend using CREATE to make it.

Hi Branislav, 

try Poptree2, it is very easy to use software freely available suited for your purpose.