There is a command line program called ROARY that has been designed for analysing core/pan genome within a species and it can build an alignment and phylogenetic tree of the core (conserved) genes of the genomes supplied.

Another option I have used in the past is to build the multiple sequence alignment for each gene using clustalw and output the alignment as the default .aln clustal format with the order of genes in the alignment conserved (same as order in the input file). the .aln format is a interleaved alignment format which if the order of the genes belonging to each genome is the same in each .aln file you can actually cut and past the alignments of each file underneath each other (or use the 'cat' command if using linux) and you should get one long multiple sequence alignment when you open the file up in an alignment viewer ( I used BioEdit at the time, haven't tested MEGA6). Although I must stress that the order of the gene strains in each alignment must be the same or you will get a chimeric alignment.

https://sanger-pathogens.github.io/Roary/

Hi,

I have extensively used MEGA...it works well and is easy to use (my opinion as an end user) then command line programs...see the error and try to get it rectified...many times the errors comes when there is some mistake in the input files..

bye

Thank you all for the help.

Have a good one