I use a Perl script to find a specific sequence, and as output I parse a fastafile containing the match sequence including a defined number of basepairs.
Now I want to do a multiple sequence alignment (e.g. ClustalW), but I want a position weight matrix as output, since for compatibility issues I need to create sequence using an R package. (instead of online tools such as weblogo)
Anyone knows a alignment tool (Bioperl, Bioconductor, online?) which gives me the matrix as output?