Hi Cristian

 Xiao Chen answer is OK. but there are many other programs and packages to do it. For your mtDNA, you coul also use some of the DNA programms in PHYLIP (http://evolution.genetics.washington.edu/phylip.html), such as DNApars, DNAmove, etc. Just be aware of the different assumptions made by the different programms. (http://evolution.genetics.washington.edu/phylip/progs.data.dna.html).

Then you can use Seqboot (shipped with PHYLIP) to get the nodes probability and plot your tree with .....

Hope this helps

Pablo

Are you comparing mtDNA from within species? Or from different species or genera? Most of my recent work has been on the phylogenetics of mitochondrial genomes; I'd be happy to share what I have found.

I recommend to use rstudio software for this analysis and better result