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#### <code>ms+seqgen</code> -- Simulation sequences according a tree.
In the following, we demonstrate the <code>ms+seqgen</code> approach
to generate sequences. The result is a character
vector of class <code>seqgen</code>, which contains 5 sequences,
each of 40 bases (<code>seq-gen</code> option <code>-l40</code>).
The option <code>-mHKY</code> specifies the HKY85
model of evolution (Hasegawa et al. 1985).
Without further options, HKY85 is equivalent to the JC69
model (Jukes and Cantor 1969).
Note that the <code>seqgen()</code> function requires a rooted tree
in NEWICK format or an object of class <code>phylo</code>.
```
> set.seed(123)
> ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
> tree.anc <- read.tree(text = ret.ms[3])
> set.seed(123)
> seqgen(opts = "-mHKY -l40", newick.tree = ret.ms[3])
5 40
s1 CTCTCATTGGACGCACACTTTAGGGGGGGATTGCACTGCA
s5 CTCTCTCTGGACGCACACTTTAAGGGGGGATTGAACTACA
s2 CTCTTCGGGCTCGGATAAGTTTGGAGGGTTGTTCTCTACA
s3 CTCTGAGTGCTCGGATTAGTTAGGGGGAATGACGTCTACA
s4 CTCTTATCTCTCGGATAAGTTGGGGGTGATGGCTTTTACA
> set.seed(123)
> (ret.seq <- seqgen(opts = "-mHKY -l40", rooted.tree = tree.anc))
5 40
s1 CTCTCATTGGACGCACACTTTAGGGGGGGATTGCACTGCA
s5 CTCTCTCTGGACGCACACTTTAAGGGGGGATTGAACTACA
s2 CTCTTCGGGCTCGGATAAGTTTGGAGGGTTGTTCTCTACA
s3 CTCTGAGTGCTCGGATTAGTTAGGGGGAATGACGTCTACA
s4 CTCTTATCTCTCGGATAAGTTGGGGGTGATGGCTTTTACA
> str(ret.seq)
Class 'seqgen' chr [1:6] " 5 40" "s1 CTCTCATTGGACGCACACTTTAGGGGGG ...
```
The following example generates a tree and provides an ancestral
sequence. Function <code>seqgen()</code> will use
parameters $\kappa$ (<code>kappa</code>) and
$\pi\_{A}, \pi\_{G}, \pi\_{C}, \pi\_{T}$
(<code>pi.HKY</code>)
to evolve the ancestral sequence
(<code>anc.HKY</code>) down the tree.
The function <code>read.seqgen()</code> reads the <code>seqgen()</code>
object and returns a new data set of class <code>seq.data</code>
for use by the function <code>phyclust()</code>.
```
> # Generate a tree
> set.seed(1234)
> ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
> tree.ms <- read.tree(text = ret.ms[3])
>
> # Generate nucleotide sequences
> (anc.HKY <- rep(0:3, 3))
[1] 0 1 2 3 0 1 2 3 0 1 2 3
> paste(nid2code(anc.HKY, lower.case = FALSE), collapse = "")
[1] "AGCTAGCTAGCT"
> pi.HKY <- c(0.2, 0.2, 0.3, 0.3)
> kappa <- 1.1
> L <- length(anc.HKY)
> set.seed(1234)
> (HKY.1 <- gen.seq.HKY(tree.ms, pi.HKY, kappa, L, anc.seq = anc.HKY))
5 12
s1 AGCTTGACCGGC
s3 AGCTTCACCGGT
s2 ACCTCGCTAGCT
s4 ACGACGCTCGCT
s5 CCTACGCTAGCT
> (ret <- read.seqgen(HKY.1))
code.type: NUCLEOTIDE, n.seq: 5, seq.len: 12.
```
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