I did multiple align for two genes, and got two multiple alignment files, each has nine sequences of the same nine species, for simplicity, I illustrate an example with 3 sequences.
Alignent 1 :
X AGCCTC Y ACCCTC Z ACGGTC
X CGGCATCC Y CCGCATAC Z AGCCATCC
Now I need to build a phylo tree from the two genes. (In fact they are rbcL and matK from chloroplast )
1) Is it correct to join them into one big alignment and estimate a plylo tree?
2) If 1) is no correct, is it possible to co-estimate a phylo tree from two alignments?
Thanks for your help