# makes a phylogeny from ASVs # phyloseq library(phyloseq) library(msa) library(DESeq2) library(dada2) library(tidyverse) # todo: filter fecal sample or let it in! # input folder input_folder <- "primer_clipped_reads_22_250250_pool" # load taxa and RSV table load(paste0("output/", input_folder, "/taxa.RData")) load(paste0("output/", input_folder, "/seqtab.RData")) # sample names samples_out <- rownames(seqtab_nochim) nes_df <- data.frame("id" = samples_out) # construct the phylogenetic tree seqs <- getSequences(seqtab_nochim) names(seqs) <- seqs # This propagates to the tip labels of the tree mult <- msa(seqs, method = "ClustalW", type = "dna", order = "input") save(mult, file = "msa_out.RData")