Hello, I am using Phylipv3.69 under Linux. I have two questions regarding generating the distance matrix using protdist:
Is there a way to output the distance matrix as a lower triangular similarity matrix, instead of a square matrix? I don't find this option within the menu for protdist.
I generated a neighbor-joining majority-rule consensus tree using seqboot->protdist->neighbor->consense. Now that the consense has picked the final tree from 100 bootstrapped tree, is there a way to go back and determine the precise distance matrix that was used to generate that tree? Or do the branch lengths on the tree suffice as the distance matrix in that case? Apologies if this seems to be a naive question, as I am not very familiar with phylogenetic analyses. The idea is that I generated two trees and I wanted to get the distance matrices of the the trees to compare them.
Thank you in advance for all your help and advice!