Could anybody help me with a building up procedure for combined data matrix? I need to combine two data matrices from DNA sequences for phylogenetic analysis. I am using MEGA for analysis.
Therefore you want to concatenate two matrices : the two matrices must have the OTUs (or species) idnetified of course by the same Ids, then you can use onlibe utilities of "FABOX" and then "Fasta alignment joiner". I used it and it works
I use SeaView (http://pbil.univ-lyon1.fr/software/seaview.html) to concatenate different markers. As Alex Baumel posted in all matrices the Ids of the taxa must be exactly de same. This seems to be a requirement of all software that allows concatenate sequences. According to your research question and the relative importance of certain taxa consider including a sequence as missing information (????????) in one of the matrices for the taxa you have not represented there.