-## mlphylo.R (2008-01-03)
+## mlphylo.R (2008-07-15)
## Estimating Phylogenies by Maximum Likelihood
stop("some branch lengths are greater than one.")
phy <- reorder(phy, "pruningwise")
if (!quiet) cat("Preparing the sequences...\n")
- BF <- if (model$model %in% 1:2) rep(0.25, 4) else base.freq(x)
if (is.list(x)) x <- as.matrix(x)
if (is.null(rownames(x)))
stop("DNA sequences have no names") # safe...
of the tree do not match") # safe here also
x <- x[phy$tip.label, ]
Y <- prepareDNA(x, model)
+ BF <- if (Y$model %in% 1:2) rep(0.25, 4) else base.freq(x)
S <- length(Y$weight)
npart <- dim(Y$partition)[2] # the number of overall partitions
## in case of negative branch lengths:
}
class(SEQ) <- "DNAbin"
- ANC <- array(1, c(nrow(SEQ) - 2, ncol(SEQ), 4))
+ ANC <- array(0, c(nrow(SEQ) - 2, ncol(SEQ), 4))
## 'partition' gives the start and end of each partition:
partition <- matrix(1, 2, npart)