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seqUtils

R-CMD-check

Tools for working with biological sequences in R.

Overview

seqUtils provides tools for common sequence analysis tasks (read & write FASTA files, translate/align/compare sequences, etc.).

Installation

You can install the development version of seqUtils from GitHub with:

# install.packages("devtools")
devtools::install_github("SamT123/seqUtils")

Requirements

  • MAFFT (for alignment)
  • cmaple (for tree building)

Example

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")
)