How to make substitution matrix?

Question

[bibilong1111]

Hi all,

 I have several sets of multiple sequence alignment, and I want to use all these sets to build a substitution matrix. 
 Could someone suggest me a easy to use R package or binary app?
 Thanks!

Answer 1

[kloetzl]

Depending on your file formats and definition of substitution matrix, maf2dist might do the trick.