[R-sig-phylo] tidytree package

Dear all, I would like to develop a tidy tool for tree manipulation. Here is what I did today: . If you have any suggestion of new verbs to be added, please don't hesitate to let me know. Best wishes, Guangchuang --

Re: [R-sig-phylo] simulate tree by specifying taxa distance

eaty Biodiversity Research Centre > University of British Columbia > Vancouver, Canada > -- > *From:* R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of Yu, > Guangchuang <g...@connect.hku.hk> > *Sent:* November 3, 2016 5:02:25 AM > *

[R-sig-phylo] simulate tree by specifying taxa distance

Dear all, I want to simulate tree with restricted taxa distances (e.g. all taxa distance should be less than 0.1). Is there any R package can do this? Best wishes, Guangchuang -- --~--~-~--~~~---~--~~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging

[R-sig-phylo] ggtree paper published

Dear all, Our R package, ggtree, had been published in Methods in Ecology and Evolution, http://onlinelibrary.wiley.com/doi/10./2041-210X.12628/abstract. The package is designed for visualizing and annotating phylogenetic tree using grammar of graphics implemented by ggplot2 package. It had

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 95, Issue 6

Dear Roger, ggtree can parse BEAST output and visualize BEAST statistics, see the document: http://www.bioconductor.org/packages/3.2/bioc/vignettes/ggtree/inst/doc/ggtree.html#annotating-tree-with-beast-output Bests, Guangchuang On Thu, Dec 10, 2015 at 7:00 PM,

[R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize?

Dear all, In the issue, https://github.com/GuangchuangYu/ggtree/issues/15, we found that midpoint() is not compatible with ladderize(). x<-rtree(10) y<-phangorn::midpoint(x) > y Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: t8, t1, t4, t6, t10, t3, ... Rooted; includes

Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize?

; y <- reorder(y) > plot(ladderize(y)) # works!!! > > Cheers, > Klaus > > > > On Sun, Oct 4, 2015 at 10:22 AM, Yu, Guangchuang <g...@connect.hku.hk> > wrote: > >> Dear all, >> >> In the issue, https://github.com/GuangchuangYu/ggtree/issues/15, w