multiModelTest: Nucleotide Substitution Models for Multiple Alignments

In oleon12/alignTools: Easy download and manage GenBank data, and alignments for phylogenetics.

Description

The function is an extension for multiple alignments of the modelTest() function from phangorn. For more information help("modelTest")

Usage

multiModelTest(
  genes,
  tree = NULL,
  model = c("JC", "F81", "HKY", "K80", "SYM", "GTR"),
  G = TRUE,
  I = TRUE,
  FREQ = FALSE,
  k = 4,
  control = pml.control(epsilon = 1e-08, maxit = 10, trace = 1),
  multicore = FALSE,
  mc.cores = NULL
)

Arguments

genes	A list objecti with multiple alignments (DNAbin class)
model	The models to evaluate. By default JC, F81, HKY, K80, SYM and GTR. Or use "all".
G	Boolean, Test Gamma. By default TRUE
I	Boolean, Test invariant sites. By default TRUE

Value

A list object of length of three. 1. summary.results: A data frame with the selected models for each alignment and each metric (AIC, AICw, AICc, AICcw and BIC). 2. results: Detailed information for each alignment (list object), the normal output of modelTest. 3. warnings: When a alignment have two o more models selected, the warning shows the models selected for each alignment and each metric.

Author(s)

Omar Daniel Leon-Alvarado [e-mail]

See Also

multiMuscle

Examples

library(alignTools)

data(Procyonidae)
head(PRocyonidae, 5L)

genes <- multiGenBank(Procyonidae, TRUE, FALSE)

alignment <- multiMuscle(genes, write.dna=FALSE)

models <- multiModelTest(genes=alignment)

models$results.summary
str(models$results)
models$results$cytb
models$warnigs

oleon12/alignTools documentation built on March 17, 2021, 4:57 p.m.