phangorn (version 1.5-0)

simSeq: Simulate sequences.

Description

Simulate sequences for a given evolutionary tree.

Usage

simSeq(tree, l=1000, Q=NULL, bf=NULL, rootseq=NULL, type="DNA",
    model="", levels=NULL, rate=1, ancestral=FALSE)

Arguments

tree

a phylogenetic tree tree, an object of class phylo.

l

length of the sequence to simulate.

Q

the rate matrix.

bf

base frequencies.

rootseq

a vector of length l containing the root sequence, other root sequence is randomly generated.

type

Type of sequences ("DNA", "AA" or "USER").

model

Amino acid models: one of "WAG", "JTT", "Dayhoff" or "LG"

levels

levels takes a character vector of the different bases, default is for nucleotide sequences, only used when type = "USER".

rate

rate.

ancestral

Return ancestral sequences?

Value

• simSeq returns an object of class phyDat.

Details

simSeq simulates sequence alignments. So far rate variation is not yet implemented, but one can combine different alignments having their own rate. In fact it is possible to generate DNA, RNA, amino acid, or 0/1.

See Also

phyDat

Examples

tree = rtree(5)
plot(tree)
nodelabels()

# Example for simple DNA alignment
data = simSeq(tree, l = 10, type="DNA", bf=c(.1,.2,.3,.4), Q=1:6)
as.character(data)

# Example to simulate discrete Gamma rate variation
rates = phangorn:::discrete.gamma(1,4)
data1 = simSeq(tree, l = 100, type="AA", model="WAG", rates[1])
data2 = simSeq(tree, l = 100, type="AA", model="WAG", rates[2])
data3 = simSeq(tree, l = 100, type="AA", model="WAG", rates[3])
data4 = simSeq(tree, l = 100, type="AA", model="WAG", rates[4])
data <- c(data1,data2, data3, data4)

write.phyDat(data, file="temp.dat", format="sequential",nbcol = -1, colsep = "")
unlink("temp.dat")