partitionfinder: PartitionFinder

In ips: Interfaces to Phylogenetic Software in R

PartitionFinder

Description

Provides a wrapper to the PartitionFinder software.

Usage

partitionfinder(
  alignment,
  user.tree,
  branchlengths = "linked",
  models = "all",
  model.selection = "BIC",
  search = "greedy",
  exec = "/Applications/PartitionFinderV1.1.1_Mac/PartitionFinder.py"
)

Arguments

alignment	A
user.tree	A
branchlengths	A
models	A
model.selection	A
search	A
exec	A character string giving the path to the executable (python script).

References

Lanfear, R., B. Calcott, S.Y.W. Ho, and S. Guindon. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695-1701.

Lanfear, R., B. Calcott, K. David, C. Mayer, and A. Stamatakis. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14: 82.

ips documentation built on May 29, 2024, 4:39 a.m.