saphy: sequential analysis of phylogenies

This package contains methods for the sequential (real-time, online) analysis of phylogenies and sequence data.

![Schema v1.0] (inst/scheme.png)

Installing the package

To install the devel version of the package, type:

devtools::install_github(c("bdearlove/treeImbalance","emvolz-phylodynamics/phydynR","Hackout3/saphy"),build_vignettes=TRUE)
#devtools::install_github("Hackout3/saphy",build_vignettes=TRUE)

Note that this requires the package devtools installed.

Note if using a mac, you will need lgfortran and lquadmath libraries installed before hand in order to compile rhydynR:

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

Contributors (by alphabetic order):

• Simon Frost (@sdwfrost)
• Don Klinkenberg (@donkeyshot)
• John Lees (@johnlees)
• Yu Luo (@yumcgill)
• OJ Watson (@OJWatson)

Maintainer (temporary): Simon Frost (sdwfrost@gmail.com)