R (>= 2.14.2), geiger, caper, ape, deSolve, matrixStats
R (>= 3.0), geiger, caper, ape, deSolve, matrixStats
caper, ape, deSolve, matrixStats, expm, picante, Matrix, DDD
(>= 3.0), stats, methods, Hmisc, DAISIE