Hi Novikov,

Based on the theory, trees can be deduced form morphological data using parsimony or Bayesian methods. You can try the MrBayes program, it can process the morphological or/and molecular data.

Hi Novikov, you can combine trees based on morphological and molecular data using PAUP software, and you can get a consensus tree.

You might want to look at the following article

Integration of Morphological Data into Molecular Phylogenetic Analysis: Toward the Identikit of the Stylasterid Ancestor

Puce S, Pica D, Schiaparelli S, Negrisolo E (2016) Integration of Morphological Data into Molecular Phylogenetic Analysis: Toward the Identikit of the Stylasterid Ancestor. PLOS ONE 11(8): e0161423. https://doi.org/10.1371/journal.pone.0161423

Dear Andriy,

if you can build two separate trees on morphology and on genetic markers, you can merge them into one by topology using supertree method. Another possible way is using Bayesian inference for both molecular data and appropriately coded morphological traits.

The comparative review on the similar issue is quite old but still be able to provide some basics ideas Article The Effect of Combining Molecular and Morphological Data in ...