This package is for making phylogenetic trees from protein sequences files with FASTA format.
To install the package, try:
devtools::install_github("MohammadTaghizadeh/REvolution")
This project beggins recently, therefore, it will go under some changes in the future.
Usage:
library(REvolution)
data(P53_sequences)
seqs <- seq_ds_matrix(P53_sequences) #select SeqFASTA
seqnames <- seq_ds_matrix(P53_sequences) #select UPID
seq_to_tree(seqs, seqnames)
Data included in this package are P53_sequences, rRNA_16S_sequences and rRNA_5S_sequences. rRNA sequences are 16S rRNA sequences which have been filtered so they are all complete sequences and not included on any N nucleotides. rRNA_5S_sequences is from RNAcentral database an small filtering has been done of deleting sequences with Ns.