The function msa() has been updated to call the executables of either MUSCLE (v3.8.31) or Clustal Omega (v1.2.4) directly from R. Further details can be found in the documentation for the msa() function. However, users are free to use alternative methods to perform the required alignments. A new vignette titled “Performing Sequence Alignment in R” has been added, providing guidance on this topic.