I am teaching myself to use the PHYLIP software to construct phylogenetic trees. Long and short is that I cannot get my consensus trees (of bootstrap replicates) to look anything like my tree inferred directly from the sequence alignments. [See attached]
The trees in the attached figure were made via Neighbor-Joining method. My workflow was as follows:
Alignment -> seqboot.exe -> bootstraps -> dnadist.exe -> distance matrix -> neighbor.exe -> NJ trees -> consense.exe -> consensus tree opened in FigTree
From what help I have found on the net, consensus trees and inferred trees are on different scales; the inferred tree scale being on measures of evolutionary distance, and consensus tree scale on measure of bootstrap frequencies (or something like that?).
What I want to know is if there is if there is a way to take the information from the consensus tree and apply to the inferred tree *within* PHYLIP? Alternatively, is there a way to take the x-number of replicate trees created and create a consensus tree in another program that will produce a phylogram that is akin to that of the inferred tree (with the correct scale)?
I am new to this software, so may have missed something... But from the tutorials I have followed I have done everything to the book.
Thank you.