-## phymltest.R (2008-10-08)
+## phymltest.R (2009-03-29)
## Fits a Bunch of Models with PhyML
-## Copyright 2004-2008 Emmanuel Paradis
+## Copyright 2004-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
os <- Sys.info()[1]
## default names of PhyML:
if (is.null(execname)) {
- if (os == "Linux") execname <- "phyml_3.0_linux32"
- if (os == "Darwin") execname <- "phyml_3.0_macintel"
- if (os == "Windows") execname <- "phyml_3.0_win32"
+ if (os == "Linux") execname <- "phyml_3.0.1_linux32"
+ if (os == "Darwin") execname <- "phyml_3.0.1_macintel"
+ if (os == "Windows") execname <- "phyml_3.0.1_win32"
}
if (is.null(execname))
stop("you must give an executable file name for PHYML")
tstv <- rep("-t e", N) # ignored by PhyML with JC69 or F81
inv <- rep(c("", "-v e"), length.out = N)
## no need to use the -c option of PhyML (4 categories by default if '-a e' is set):
- alpha <- rep(rep(c("", "-a e"), each = 2), length.out = N)
+ alpha <- rep(rep(c("-c 1", "-a e"), each = 2), length.out = N)
tree <- rep("", N)
if (!is.null(itree)) tree[] <- paste("-u ", itree)