What is a good software for ancestral trait reconstructions, and to test for phylogenetic signal.
Is Bayestraits an outdated method?
I believe Bayestraits is OK to use. Personally I use BEAST because it allows for e.g. age constraints to be included in the same analysis. BEAST cannot test for phylogenetic signal, but whether there is one becomes evident from the output of the analysis, anyway.
thanks Thomas!
Do you think a multistate discrete ancestral reconstruction or a continuous state reconstruction is possible in BEAST?? I'm looking at color evolution as means of hues and brightness values in a phylogenetic perspective.
Hi Thilina,
In BEAST, you can do ancestral state reconstruction for both continuous and discrete traits.
You may also want to look into some of the R packages. 'Phylotools' lets you do the ancestral state reconstructions (including continuous traits) as well as test for the phylogenetic signal...so, this may be a better option for you.
'Diversitree' is another R package that you can use for the ASR of a continuous trait.
Cheers,
Oksana
HI Thilina,
I recommend you BayesTraits, it has been developed specifically for that purpose with several useful features; also the previously mentioned R packages are very good and flexible. Diversitree allows you to test possible effects of traits on speciation and extinction rates.
Hi Gerardo!
Do you think one can perform a phylogenetic generalized least square regression on Bayestraits? and incorporate phylogenetic signal as well?
Hi Thilina,
I think you can do so for continuous traits, I haven't tried it. For phylogenetic signal, personally I have tried Pagel's lambda and Blomberg's K parameters, both can be estimated in Phytools, whereas Diversitree only estimates lambda.
Cheers
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