Thread Safe C/C++ Libraries For Sequence Alignment

Question

[Tianyang Li]

Hi,

Are there thread safe C/C++ library for sequence alignment?

I was checking out Seqan, but in the documentation it wasn't explicitly stated that it's thread safe for alignments.

I'm wondering if there are other libraries available?

Thanks!

Answer 1

[Bill Pearson]

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

Answer 2

[Tianyang Li]

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