In choosing the methods for our study, we only considered the availability of software and the simplicity of implementing the alignment scoring functions (see the Results section).
The authors used a custom Haskell embedding of algebraic DP to implement the alignment algorithm for rapid prototyping, easy evaluation of the scoring function and optimizations.
We chose to demonstrate examples for AGE, CrossMatch (http://www.phrap.org/phredphrapconsed.html, implementing the Smith Waterman alignment), GAP3 (Huang and Chao, 2003) (implementing a generalized global alignment with piecewise gap penalty), and Blat (Kent, 2002), a popular heuristic alignment program aimed at aligning highly similar sequences with large gaps.
We implemented the delay alignment and phase rotation modules on a Texas Instruments C6678 DSP with 8 cores.
In this study, two methods are implemented: the sequence alignment method based on the BLASTP and the feature selection method with amino acid composition and pseudo amino acid composition features [90].
An R-package implementing the graph alignment is available from the bioconductor website [ 36].
Rip sequences were aligned using the ProGraphMSA program, which implements the evolution-aware alignment [ 65, 66].
The sequences were first aligned with ClustalW implemented in BioEdit and the alignment was then refined by eye (total 1097 nucleotidic sites, see Suppl. Figure 1) [ 39].
Nucleotide and protein sequences were aligned using the Alignment Explorer/CLUSTALW [ 53] implemented in Molecular Evolutionary Genetics Analysis MEGAA version 4.0) [ 54].
Among the various algorithms for aligning multiple sequences, we selected the alignment approach implemented in the PRANK program [16].
