satDNA Analyzer

Current Released Version: 1.2 (October, 2006)

satDNA Analyzer (satellite-DNA Analyzer), is a software package for the analysis of satellite-DNA sequences from aligned DNA sequence data. It allows 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 two 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. (1985) 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 rate, and different estimates of intra 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 an alignment to be used for further evolutionary analysis by using different phylogenetic softwares. The novelty of this feature is that it allows to discard the shared polymorphisms for the analysis, which we have demonstrated can interfere with the results when analyzing closely related species (Navajas-Perez et al., 2005).

satDNA Analyzer Features

1.- Sequence Translator

satDNA Analyzer reads and outputs most common sequence formats. This software uses the SEQIO.


J. Knight
 (1996). SEQIO: A Package for Reading and Writing Sequence Files, distributed by the author.

2.- Transition-Stages Finder

The program recognizes different positions and transition stages, according to the following scheme:

  1. Non-monomorphic positions: POLYMORPHISM:
    1. Both species share at least two nucleotides: Shared polymorphism.
    2. Both species share up to one nucleotide: Non-shared polymorphisms sensu lato. 
      1. No fixed positions in any species: Irrelevant positions.
      3. One fixed position: Variable Transition States (VTS).
        1. Indels included: Irrelevant positions with indels.
        2. No indels: Strachan Transition States (STS):
          • STS-II: mutation in one species spread up to 25% of sequences.
          • STS-III: mutation in one species spread between 25-50% of sequences.
          • STS-IV: mutation in one species spread between 50-100% of sequences.
          • STS-V: different nucleotides fixed in each species.
          • STS-VI: a new cycle of mutation-homogenization starts.
  3. Monomorphic position: STS I.

3.- Estimates of DNA Divergence Between Species

The program estimates the following measures for each individual species:


And considering the two species:


Lynch, M. & Crease, T J.
(1990). The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol., 7:377-394.
Nei, M.
(1987). Molecular Evolutionary Genetics. Columbia University Press, New York, NY.
Tajima, F.
(1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105:437-460.

4.- Removing shared polymorphisms from alignment

SatDNA Analyzer generates an output file alingment without shared polymorphisms to be used in further phylogenetic analysis. We have recently proposed a model for the analysis of satellite-DNA sequences of closely related species (Navajas-Perez et al., 2005). We propose there that shared polymorphisms are ancestral variation prior to species spliting and therefore they could interfere with the results. In contrast, nonshared polymophisms are automorphies, representing different transitional stages in the proccess of intraspecific sequence homogenization and interspecific divergence. So, shared polymorphisms should be excluded in some cases from the alignment to allow more accurate calculations.


R. Navajas-Pérez, R. de la Herrán, C. Ruiz Rejón, M. Jamilena, R. Lozano, C. Ruiz Rejón, M. Ruiz Rejón & M. A. Garrido-Ramos
 (2005). Reduced rates of sequence evolution of Y-linked satellite DNA in Rumex (Polygonaceae). J. Mol. Evol. (2005) 60:391-399