[R-sig-phylo] Fully annotated phylogeny using R?

Hi all I would really like to see an example of code for a fully annotated phylogeny done using R if anyone has it? Say combining symbols, words, related empirical data? Or alternatively tell me its too hard and there are better programs out there? Hopefully, Chris Buddenhagen Florida State

[R-sig-phylo] Does possession of a character state affect number of regions occupied or rate of diversification?

occur in all regions, most in two, some in one. Can I use this data and my time calibrated beast tree to reconstruct ancestral areas in R? Cheers Chris Buddenhagen Florida State University [[alternative HTML version deleted]] ___ R-sig-phylo

[R-sig-phylo] pairwise comparisons of 100s of gene tree topologies

. Best Chris Buddenhagen Florida State University cbuddenha...@gmail.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http

[R-sig-phylo] Is there an existing method for tallying relationships between 3 clades for 100s of trees?

with the following fields. Loci# (taken from file name), Relationship Supported, Support Value for the relationship Any ideas? Hopefully Chris Buddenhagen FSU cbuddenha...@gmail.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing

[R-sig-phylo] Pairwise genetic distances for many genes and taxa

pairs (with cells containing genetic distances for each combination). I have 100s of loci either as separate phylip files or as a single concatenated phylip file with a separate file specifying locus coordinates. Any ideas how I could quickly generate the matrix? Sincerely Chris Buddenhagen Florida

[R-sig-phylo] Determining the most informative regions for a selected clade

Given a tree is there a way to determine which DNA regions best explain clade membership within user selected clades on a tree? This would be within 261 loci represented by multiple alignments or a partitioned concatenation? [[alternative HTML version deleted]]

[R-sig-phylo] get mean support and sd for 100s of gene trees - also node match counting gene trees vs reference

ay to use a reference total evidence tree and get an idea how many gene trees support the same descendants (tip members) for a node? Then maybe do the same and take into account that not all gene trees have the same tips? Perhaps pruning the total evidence tree to the shared taxa in the gene t

[R-sig-phylo] 3 dimensional ordination of tree distances

Is there a way to plot gene tree similarities in 3D ordinal space? I want to identify groups and outliers for hundreds of gene trees. I am pretty happy with TreeCmp (java program and graphing distances in ggplot) but I'd be keen to see this in a more multi-dimensional format. Cheers Chris

[R-sig-phylo] Mirrored trees with connecting lines between taxa that are not in matching locations

I want to visually compare topologies between a chloroplast & nuclear DNA derived trees. I remember a post where some r code/package is available to draw mirrored trees with lines between taxa that are non-matching between them. Please can someone remind me about this package? Hopefully, C

[R-sig-phylo] Associated r created graphs or external images with specific nodes on a phylogeny

Is there a way to quickly associate a small graph created in R with each node on a tree and have the graphic appear on the node when plotted? Or alternatively is there a way to get out the node coordinates of each node for a given plot? Sincerely Chris Buddenhagen cbuddenha...@gmail.com

[R-sig-phylo] chronos ape package does it return confidence intervals too?

Just this quick question Chris Buddenhagen cbuddenha...@gmail.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 106, Issue 15

I found the java software package TreeCmp to be very good with the pruning function implemented: Bogdanowicz, Damian, Krzysztof Giaro, and Borys Wróbel. “TreeCmp: Comparison of Trees in Polynomial Time.” *Evolutionary Bioinformatics Online* 8 (2012): 475–87. Chris Buddenhagen cbuddenha