I extended usual BLOSUM alphabet with my own letter. And has scores for it.

Now looking for an alignement tool that can make Global Multiple Allignement with my score matrix.

I have:

• file weight 4 mb
• 10 seqs
• max length 721226 amino acids
• avg length 367777 amino acids

Tried:

• Clustal O. It doesn't except matrix. Checked sources - didn't find ability.
• Clustal W. Works too long, mb good variant.
• MAFFT. Can't extend alphabet for it. Even if specify letter in my BLOSUM text file (unknown letter).
• MUSCLE. Memory limits. Wants to allocate 4gb of memory.

Maybe i didn't see abilities in these tools. Will be glad of any help.