The alignment functions in the fasta package (http://faculty.virginia.edu/wrpearson/fasta) are thread safe, and you are welcome to use the alignment functions you need (e.g. do_walign() in the dropgsw2.c file for Smith-Waterman, or bd_align() for banded local alignment, or any of the functions in wm_align.c). Unfortunately, they are not very well documented, but their overall structure is relatively simple.

They are definitely thread safe; both the score functions and alignment functions in the FASTA package are fully threaded.

Bill Pearson

Seqan's alignment's OK for multi-threading. Here's what one of the authors said.