I am quite new to phylogenetic analysis. Please bare with me if question does not make sense.
I am using IQtree to analyse some horizontally transferred genes. I have successfully generated phylogenetic tree using IQtree. I have few questions related to interpretation of the trees given by IQtree.
1). I want to find relatedness between each pair of species in the tree. In simple terms, I want pair wise distance matrix. To do this, first, I converted unrooted tree to rooted tree using outgroup sequence. Question is, how can I get the pairwise distance of rooted phylogenetic tree ?? I know IQtree gives .mldist file having pairwise distance matrix of final tree given by IQtree. However, I don't know how much the matrix of .mldist file is reliable to use if I converted original unrooted tree to rooted tree ??
Any answer would be highly highly appreciated.