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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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