[Bio-software] Pairwise alignements versus multiple alignement for distance matrix

[Ahmed Moustafa]

Dear All,

Generally distance-based tree construction methods begin with multiple
sequence alignment for the protein sequences and than measuring the
distances between each two sequences in the alignment to fill in the
distance matrix.

My question is why not rather than performing the multiple sequence
alignment, simply use pairwise alignments scores to fill in the
distance matrix and from there to construct and infer the tree.

Thanks in advance!

Ahmed