buildSeqTree: Build a phylogenetic tree
In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

buildSeqTree

R Documentation

Build a phylogenetic tree

Description

Build a phylogenetic tree

Usage

buildSeqTree(
  x,
  pml_model = "GTR",
  pml_optInv = TRUE,
  pml_optGamma = TRUE,
  pml_rearrangement = "stochastic",
  pml_control = pml.control(trace = 0)
)

Arguments

`x`	Sequences DNAStringSet
`pml_model`	See optim.pml `phangorn`
`pml_optInv`	See optim.pml `phangorn`
`pml_optGamma`	See optim.pml `phangorn`
`pml_rearrangement`	See optim.pml `phangorn` #'
`pml_control`	See optim.pml `phangorn`

Details

A wrapper to build phylogenetic tree for ASV sequences obtained after dada2.

Examples

library(biomeUtils)
data("SprockettTHData")
# select few for example
seqs <- sample(SprockettTHData@refseq, 5)
sp.tree <- buildSeqTree(seqs)
sp.tree$tree

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.