I am using Compare 4.6 software to perform PGLS on a large set of trait values using a known phylogeny (based on genetic distance; Taxa = 23, Traits = 110, phylogeny = 1). The problem is that when I include the phylogeny in Nexus format, all results are 0 except for Mean(TIPS). This is confusing as alpha = 0 indicating that phylogenetic signal is strong and therefore Mean(TIPS) values are irrelevant. Should I accept these results as they are or could an error on my part be responsible for this outcome?
When I choose to generate trees within Compare4.6 (based on trait distance) and then modify branch positions according to the true phylogeny, none of my changes are registered in the phylogeny box. Executing an analysis yields results that make a lot more sense than using the known phylogeny but I cannot use them as they are not based on the true phylogeny. How can I get the software to register my adjustments to the simulated phylogenies?
Apologies for any lack of clarity in my explanation. I have a very rudimentary understanding of the method and software. If anyone can provide guidance, it would be tremendously appreciated.
I do not use Compare but wonder if you could simply open the phylogenetic tree in FigTree and format it it as you wish. Then save an eps, pdf or jpeg from Figtree to a graphics program and add text or symbols from the Compare results to the the phylogenetic tree.
I almost always go through a process like this because info contained in a tree I need does not necessarily show up in the phylogeny that I use for a figure. I work on a Mac and use Intaglio, which is very affordable so that I can save the final tree figure in a form that the journal would like.
Please clarify if I am not understanding the problem. Also could you possibly use a phylogeny based on maximum likelihood rather than distance? Perhaps not necessary for your journal but ML is really a much better way to do a phylogeny.
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics