in my current odessey through phylogeny and multiple sequence alignments I came across another question I hope to be answered.
I did MSA with different algorithms from MAFFT, MUSCLE and compared the trees calculated from these alignments with the tree calculated from the original Pfam alignment (I wanted to try ProbCons as well, but neither their web interface nor the local install worked for me). Now, the overall tree structure looks similar, but rearrangements of subgroups/clades are present.
However, the trees calculated from MAFFT with FFT-NS-i, L-NS-i and Pfam look identical. Those from MUSCLE and MAFFT with E-NS-i are also nearly identical to each other. MAFFT with global alignment approach G-NS-i looks different from all others. Basically I used six different algorithms and ended up with tree different trees, with three alignments resulting in the same tree, two in the another same and a third from one.
Now, since I'm just a interested microbiologist for me the differences are hard to interpret, although I expected to see some small difference. Is one alignment more 'true' than the other, when different algorithms result in the same tree?