FastME {ape} | R Documentation |
The two FastME functions (balanced and OLS) perform the Minimum Evolution algorithm of Desper and Gascuel (2002).
fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE) fastme.ols(X, nni = TRUE)
X |
a distance matrix; may be an object of class "dist" . |
nni |
a boolean value; TRUE to do NNIs (default). |
spr |
ditto for SPRs. |
tbr |
ditto for TBRs. |
an object of class "phylo"
.
original C code by Richard Desper; adapted and ported to R by Vincent Lefort vincent.lefort@lirmm.fr
Desper, R. and Gascuel, O. (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Journal of Computational Biology, 9(5), 687–705.
nj
, bionj
,
write.tree
, read.tree
,
dist.dna
, mlphylo
### From Saitou and Nei (1987, Table 1): x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13, 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12, 5, 6, 10, 9, 13, 8) M <- matrix(0, 8, 8) M[row(M) > col(M)] <- x M[row(M) < col(M)] <- x rownames(M) <- colnames(M) <- 1:8 tr <- fastme.bal(M) plot(tr, "u") ### a less theoretical example data(woodmouse) trw <- fastme.bal(dist.dna(woodmouse)) plot(trw)