README.md

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

Rboretum: Comparisons and Visualizations of Phylogenetic Tree Topology and Alignment Support in R

Dr. Bob Literman Dr. Rachel Schwartz University of Rhode Island

v.1.0 (01/01/2020)

Program Dependencies

• R version >= 3.6.1
• Python version >= 3.6+ w/Biopython

R Package Dependencies

• ape (>= 5.4.1)
• phytools (>= 0.6.99)
• phangorn (>= 2.5.5)
• testit (>= 0.9)
• tidyverse (>= 1.2.1)
• tools (>= 3.6.1)
• reticulate (>= 1.13)
• scales (>= 1.0.0)
• viridis (>= 0.5.1)
• cowplot (>= 1.0.0)
• ggtree (>= 1.16.6)
• ggimage
• grDevices (>= 3.6.1)
• viridisLite (>= 0.3.0)
• rlist (>= 0.4.6.1)
• BiocManager (>= 1.30.10)

Rboretum Installation

library(devtools)
devtools::install_github("BobLiterman/Rboretum",build_vignettes=TRUE)

Note that if you have any problems relating to the installation of reticulate see the following issue.

Loading Library

library(Rboretum)
sourceRboretum()

Rboretum is very much a work in progress, and raising early issues would be very helpful. What do you wish you could easily do in R? Let me know and I'll try to make it happen for you.

For basic usage, please: - See the associated vignette. vignette(package="Rboretum", "vignette") - Visit the ReadTheDocs (under construction)

Feel free to reach out to me on Twitter (@BobLiterman) or over e-mail ([e-mail])

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.