SciPhy was designed to construct maximum likelihood phylogenetic trees for amino acid sequences. The SciPhy conceptual workflow is composed by the following main activities: (1) Alignment Construction: with MAFFT, (2) Alignment Format Conversion: with ReadSeq, (3) Best Evolutionary Model Election: with ModelGenerator, and (4) Phylogenetic Tree Construction: with RAxML
SwiftGecko identifies collections of high-scoring segment pairs (HSPs) in genomes. The SwiftGecko conceptual workflow is composed by three computational modulesm, covering ten main activities: (I) Dictionary Calculation, for creatimg dictionaries for each sequence, composed by activities: (1) Reverse Complementary Sequence, (2) Words Scanning (3), Words Sorting, and (4) Computing Genome Dictionaries. (II) HSP Detection, for detecting seed points or hits used to identify HSP locations, composed by activities (5) Hits Detection, (6) Hits Sorting, (7) Hits Filtering, (8) Fragment Obtaining, and (9) Combine Fragments. (III) Post-processing Module, for attaching complementary tasks for performing statistical calculations, composed by activity: (10) CSV File Generation.