title: SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis.
abstract: satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism according to the model proposed by Strachan et al. in six different stages of transition during the spread of a variant repeat unit toward its fixation. Furthermore, this program implements several other utilities for satellite-DNA analysis evolution such as the design of the average consensus sequences, the average base pair contents, the distribution of variant sites, the transition to transversion ratio and different estimates of intra-specific variation and inter-specific variation. Aprioristic hypotheses on factors influencing the molecular drive process and the rates and biases of concerted evolution can be tested with this program. Additionally, satDNA Analyzer generates an output file containing a sequence alignment without shared polymorphisms to be used for further evolutionary analysis by using different phylogenetic softwares.
  
  
  BACKGROUND
  satDNA Analyzer is freely available at http://satdna.sourceforge.net/. SatDNA Analyzer has been designed to operate on Windows, Linux and Mac OS X.
authors.affiliation: Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain. rnavajas@uga.edu
authors.forename: Rafael
authors.initials: R
authors.lastname: Navajas-Pérez
authors.forename: Cristina
authors.initials: C
authors.lastname: Rubio-Escudero
authors.forename: José Luis
authors.initials: JL
authors.lastname: Aznarte
authors.forename: Manuel Ruiz
authors.initials: MR
authors.lastname: Rejón
authors.forename: Manuel A
authors.initials: MA
authors.lastname: Garrido-Ramos
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D004276:DNA, Satellite / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D004276:DNA, Satellite