partitionfinder {ips}

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.