You should use Mesquite, which is a free program. This program allows you to make the alignments and also, to concatenate matrices. The process to interpretate a phylogenetic tree or how to make the concatenation of different matrices is not easy to explain here.

Thank you for your suggestion. kindly recommend some basic articles recarding construction of concanated Phylogenetic tree sir, once again thanks for your kind reply sir

Hi, you can also use MEGA to concatenate multiple genes for phylogenetic analysis. It is not that simple but

Basicly

-align sequences of each gene and save

-import the alignment file of each gene by using analyze button

-transform the meg format