title: SWAPSC: sliding window analysis procedure to detect selective constraints.
abstract: Sliding-window analysis procedure to detect selective constraints (SWAPSC) is a software system to dissect the constraints on the evolution of protein-coding genes. The program estimates rates of nucleotide substitutions at specific codon regions in each branch of a phylogenetic tree. The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and non-synonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints. Finally, the optimum window size is slid along the real alignment and a test for significance of the estimated number of synonymous and non-synonymous nucleotide substitutions in each sliding step is conducted. A number of friendly useful output files is generated.
  
  
  BACKGROUND
  SWAPSC is available at http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml distribution versions for both Linux and Windows operating systems are available, including manual and example files.
authors.affiliation: Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland. mario.fares@may.ie
authors.forename: Mario A
authors.initials: MA
authors.lastname: Fares
mesh_terms: D000465:Algorithms; D004252:DNA Mutational Analysis / Q000379:methods*; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D019143:Evolution, Molecular; D014644:Genetic Variation; D016247:Information Storage and Retrieval / Q000379:methods*; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software