estimatePhangornTree: Estimate a ML tree from a given topology Uses 'pml' and...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Estimate a ML tree from a given topology Uses 'pml' and 'optim.pml' from the 'phangorn' package to estimate the tree.

Description

Estimate a ML tree from a given topology Uses 'pml' and 'optim.pml' from the 'phangorn' package to estimate the tree.

Usage

estimatePhangornTree(
  alnfile,
  treefile,
  submodel = "LG",
  type = "AA",
  format = "fasta",
  k = 4,
  ...
)

Arguments

alnfile	The path to the sequence alignment file
treefile	The path to the master tree file (whose topology will be used to generate the tree)
submodel	Substitution model to be used to estimate the tree
type	"AA" for amino acid or "DNA" for DNA
format	Format of the alignment file (commonly used formats include fasta and phylip)
k	Number of intervals in the discrete gamma distribution for 'pml'
...	Further arguments passed to 'pml' or 'optim.pml'

Value

A list: 'tree.opt' is the tree from the optimized output of 'optim.pml'; 'results.opt' is the optimized output of 'optim.pml'; 'results.init' is the initial results estimated by 'pml'

See Also

phyDat for alignment formats, pml and optim.pml for tree estimation

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.