Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R?

Question

[audrey]

Hi, I am working on multiple sequence alignments and I want to obtain the number of aligned sites between each pair of aligned sequences (in other words, the length of the alignment between each pair of aligned sequences, preferentially in a matrix). I am working in R, with DECIPHER and sequinR packages, and could not find any appropriate function in these packages nor online. Is there any package or function that does this, or do I have to code it from scratch?