Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Thank you everyone for your help, I really appreciate it! On Wed, Jul 26, 2017 at 11:55 AM, Jarrod Hadfield wrote: > Hi Jesse, > > In order to account for phylogenetic uncertainty you are better just > pulling trees from their posterior rather than choosing trees that are >

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, In order to account for phylogenetic uncertainty you are better just pulling trees from their posterior rather than choosing trees that are incongruent. The latter will give estimates biased toward those associated with extreme trees. If the analysis is the binomial model you

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, there is a function maxCladeCred() to compute maximum-clade-credibility in phangorn, if you prefer doing it in R. In the package are several distances between trees implemented see ?RF.dist (treespace uses them internally). Klaus On Wed, Jul 26, 2017 at 11:06 AM, Santiago Sánchez <

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, As Eduardo says, if in fact you want to see how different trees are from a "consensus", something that you could try is find the maximum-clade-credibility (MCC) tree (you can do this with treeAnnotator from BEAST). This will be a fully bifurcating tree and is essentially the tree in the

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, Do you want to select the trees that are most incongruent with some sort of average of the tree distribution? The `treespace`and `phytools` packages have functions that compute average trees with different metrics, and they also allow you to measure the distance between each tree and