Hi Simone,

The best software for to produce cladograms from a binary matrix is by far TNT, a parsimony program. Find it here:

http://www.lillo.org.ar/phylogeny/tnt/

Cheers,

Camilo

Hello, Simone!

Did you try Beast? http://www.beast2.org/

Could you please explain why are you using binary data and not the sequence itself?

The R package Phangorn (http://cran.r-project.org/web/packages/phangorn/index.html) allows doing that.

Hi Simone,

The best software for to produce cladograms from a binary matrix is by far TNT, a parsimony program. Find it here:

http://www.lillo.org.ar/phylogeny/tnt/

Cheers,

Camilo

+1 for TNT. It is likely to be the easiest way to do this and will have the simplest interpretation given the lack of complicated models.

I agree with Camilo and Rob.  If you want to make a cladogram, you need to use software that does parsimony analysis.  Other methods that are not based on parsimony produce phylogenetic trees, but they are not cladigrams.

Hi Simone !

Based on your presence/absence matrix (0/1) of known mutation, you can construct a dendrogram using several methods (e.g : Neighbour-Joining ), distances (Jaccard or Euclidean etc) and bootstrapping with PAST software (Past 3.x - the Past of the Future).

Here is the link : http://folk.uio.no/ohammer/past/

All the best,

I agree with Andrew Brower. So, I prefer to use methods that produce phylogenetics tree. Dear Simone, you can try to describe the characters instead to use only present/absent. Your phylogenetic proposal will be more informative and coerent. I use TNT too, more with (0) for plesiomorphic state, and (1, 2.....) for apomorphici state. Good luck.