phyformat: phyformat: A package to help bioinformatics data formatting
In yh986/PhyFormat: Format Bioinformatics Data

phyformat provides the ability to read and write sequence data in FASTA and PHYLIP formats, including the ability to interconvert between the two. It also includes a function to take a subset of a Newick-format phylogenetic tree.

x <- ReadFasta("sequences.fa") #Creates a physeq object from an existing FASTA file
x$Sequences[[1]] <- "PQHLIRV" #Edit a sequence in the physeq object
WriteFasta(x, "sequences2.fa") #Write to a fasta file
WritePhylip(x, "sequences2.phy") #Write to a PHYLIP file

y <- physeq(c("Seq 1", "Seq 2"), c("RRARRPR", "PKKKRKV")) #Creates a physeq object