phylo_tree_with_FastTree.R

# phylogenetic tree options
# using fasttree

# load packages
library(phyloseq)
library(tidyr)
library(dplyr)
library(dada2)

# NEED TO INSTALL FASTTREE

# load in alignment file ####
myalignment <- read.dna("where/alignment/file/is.fasta",format="fasta",as.matrix=TRUE)

# run using FastTree
system('~/where/FastTree/is/FastTree -nt where/alignment/file/is.fasta > where/to/save/alignment/tree')
# this took 14 minutes

# load in data needed for the phyloseq objects
seqtab <- readRDS('where/seqtab/is/seqtab.rds')
meta <- read.csv('where/metadata/is/metadata.csv')
taxtab <- readRDS('where/taxtab/is/taxtab.rds')
tree <- read_tree('where/tree/is/tree')

# change row names
rownames(meta) <- meta$SampleID

# make phyloseq object
ps <-phyloseq(tax_table(taxtab),
sample_data(meta),
otu_table(seqtab, taxa_are_rows = FALSE),
phy_tree(tree))

# overwrite previous phyloseq object
saveRDS(ps, 'where/to/save/phyloseq/object/ps.rds')