mlandis

#NEXUS

Begin data;
Dimensions ntax=3 nchar=5;
Format datatype=DNA missing=? gap=-;
Matrix
A   CTGAA
B   TCCCG
C   CAAAC
;

mlandis

# read in the data
data <- readDiscreteCharacterData(data_filename)

# read in a tree (this could also be a stochastic tree variable)
tree <- readTrees(tree_filename)[1]

# assign a lognormal prior to the transition/transversion rate
kappa_sd <- 1.0
kappa_mean <- -0.5 * kappa_sd^2
kappa ~ dnLognormal(kappa_mean, kappa_sd)

mlandis

# io
fp = "./"
fn = fp + "prior_unrooted.txt"

# make a tree variable
n_tips = 10
for (i in 1:n_tips) { names[i] = "T"+i }
t ~ dnUniformTopology(nTaxa=n_tips, names=names)

# create a vector of moves

mlandis

# io
fp = "./"
fn = fp + "prior_timetree.txt"

# make a tree variable
n_tips = 10
for (i in 1:n_tips) { names[i] = "T"+i }
t ~ dnUniformTimeTree(originTime=1.0, taxonNames=names)

# create a vector of moves

mlandis

> brew doctor
Your system is ready to brew.

> brew --config
HOMEBREW_VERSION: 0.9.4
ORIGIN: https://github.com/mxcl/homebrew
HEAD: de885ecdb0889d1246eda3621cb5d89d46130b7e
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 16-core 64-bit nehalem