Will SnapGene Tools run multithreaded?
SnapGene can run some operations in parallel on a computer with a multiple core CPU.
Pairwise and Multiple Alignments
SnapGene bundles and uses a numbers of executables for alignment algorithms (MAAFT, Clustal Omega, Muscle, T-Coffee, Parasail).
The MAFFT Algorithm can use multiple cores for faster computation of alignments. By default it will use the appropriate number of available cores.
All other pairwise and multiple alignment algorithms are written and compiled to run on a single core.
If you choose to run multiple alignment algorithms at once, then each will run in parallel in a separate core.
Alignment to a Reference
The "Alignment to Reference" tool runs on a single core. It is designed primarily for validating independent sequences against a reference. It should not be used with more than a few hundred aligned sequences.
De novo Assembly
SnapGene bundles the CAP3 algorithm for de novo assembly of reads into contigs (see De Novo Assembly of Sanger Sequences). The CAP3 algorithm is not multithreaded. We provide the CAP3 tool for generation of Sanger read assemblies, we do not recommend it be used with large (more that a few hundred reads) fastq or Sanger datasets.