Tools for working with biological sequences in R.
seqUtils provides tools for common sequence analysis tasks (read &
write FASTA files, translate/align/compare sequences, etc.).
You can install the development version of seqUtils from GitHub with:
# install.packages("devtools")
devtools::install_github("SamT123/seqUtils")- MAFFT (for alignment)
- cmaple (for tree building)
library(seqUtils)
# Read FASTA file
sequences <- fast_fasta("sequences.fasta")
# Translate to amino acids
aa_sequences <- translate(sequences)
# Find substitutions compared to a reference
substitutions <- get_substitutions(
reference_seq,
query_seqs,
exclude = c("X", "N")
)