infer_phylogeny {nodeSub}

infer the time calibrated phylogeny associated with the provided alignment. This function uses the R package babette to infer the phylogeny using BEAST2.

Description

infer the time calibrated phylogeny associated with the provided alignment. This function uses the R package babette to infer the phylogeny using BEAST2.

Usage

infer_phylogeny(
  alignment,
  treatment_name,
  tree_prior = beautier::create_bd_tree_prior(),
  clock_prior = beautier::create_strict_clock_model(),
  mcmc_seed = NULL,
  chain_length = 1e+07,
  sample_interval = 5000,
  burnin = 0.1,
  working_dir = NULL,
  sub_rate = 1
)

Arguments

alignment

Phydat object containing the focal alignment

treatment_name

string to be appended to BEAST files

tree_prior

tree prior used, default = birth-death prior

clock_prior

clock prior used, default = strict clock

mcmc_seed

seed of the mcmc chain, default is the system time

chain_length

length of the mcmc chain, default is 1e7.

sample_interval

interval of sampling, default is 5000

burnin

burnin of posterior distribution

working_dir

beast2 working dir

sub_rate

substitution rate used to generate the original alignment (if available), default is 1

Value

list with all trees, and the consensus tree