Make.Tree.QIIME: Make.Tree

In jbisanz/MicrobeR: Handy functions for microbiome analysis in R

Description

Takes a series of sequences and uses muscle and make_phylogeny (Make.Tree.QIIME) OR DECIPHER and phangorn (Make.Tree.R) as per https://f1000research.com/articles/5-1492/v2. The R-method will take considerably longer and becomes unusable for >a few hundred features. For QIIME method: can be used with MacQIIME or QIIME. Will default to MacQIIME locations. A file called Feature_Seqs.tree will be created in your working directory for future use. Uses midpoint rooting, and fasttree. NOTE: This is using system commands... probabily will only work on mac and linux. If you are using windows reconsider your life choices and consider dual booting Ubuntu.

Usage

Make.Tree.QIIME(FEATURENAMES, FEATURESEQS, MUSCLE, MAKEPHY, PRINTTREE)

Arguments

FEATURENAMES	The names of your features/OTUs/SVs. Will be the row names of your input table in most cases.
FEATURESEQS	The corresponding sequences for each feature. If this is a dada2 table, then feature names are also feature seqs.
MUSCLE	(optional) The location of muscle, defaults to /macqiime/bin/muscle
MAKEPHY	(optional) Location of qiime make_phylogeny.py, defatuls to /macqiime/anaconda/bin/make_phylogeny.py
PRINTTREE	(optional) Would you like a tree to be printed TRUE/FALSE? defaults to TRUE

Details

Generate a phylogenetic tree and optional plot.

Value

Returns tree object and prints a phylogenetic tree

jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.