Saturday, April 2, 2016

Species tree method update: iGTP

iGTP - short for Gene Tree Parsimony - is a highly specialised software for the inference of species trees from gene trees using parsimony criteria. It offers the criteria Minimising Deep Coalescences (MDC) to deal with incomplete lineage sorting and Minimising Gene Duplications as well as Minimising Gene Duplications and Losses for when dealing with gene families.

Input data are all the gene trees in Newick format in one text file. Several alleles or individuals in the same species should have the exact same name, which is rather unusual. Most other species tree programs use allele assignment tables.

Sadly it failed to work on Ubuntu at home; it started but did not actually do anything after importing the gene trees. Yesterday I finally gave iGTP a try on Windows. It worked fine with exactly the same gene tree file as I tried on Ubuntu, further demonstrating that there is something wrong with the Linux version I downloaded.

So how did it go? The program is fast and simple to use, but there are two little problems. First, it produced a very different tree for the same dataset than did *BEAST and ASTRAL, and the solutions found by the latter two make considerably more sense in the light of the morphology and biogeography of the species in question. I am afraid in this case MDC may have been mislead.

Second, iGTP has an integrated tree viewer that I found both unnecessarily complicated and, sorry to be so frank, ugly. Complicated in that it is some kind of fancy 3d viewer where a simple FigTree/TreeView style representation would be more helpful, and ugly in that the semi-transparent white font on an intensely blue background hurt my eyes. Seriously, I could barely make out the species names.

MDC is known to find the wrong answer under a very specific set of circumstances (just like parsimony on a single character matrix has a problem with long branch attraction), and maybe that is what is happening here. I am sure there are many cases where it will work better; in fact in the past I have often found that MDC and *BEAST would produce meaningful results where algorithmic/distance based approaches similar to ASTRAL would produce nonsense. But in this specific case I will leave it at having tried out how iGTP works.

Will update the big species tree post to include these new observations.

No comments:

Post a Comment