Arvestad L; Bruno WJ.
     Estimation of reversible substitution matrices from multiple pairs of
     sequences.
   Journal of Molecular Evolution, 1997 Dec, 45(6):696-703.
       (UI:  98080643)
 
Abstract: We present a method for estimating the most general reversible
    substitution matrix corresponding to a given collection of pairwise aligned
    DNA sequences. This matrix can then be used to calculate evolutionary
    distances between pairs of sequences in the collection. If only two
    sequences are considered, our method is equivalent to that of Lanave et al.
    (1984). The main novelty of our approach is in combining data from
    different sequence pairs. We describe a weighting method for pairs of taxa
    related by a known tree that results in uniform weights for all branches.
    Our method for estimating the rate matrix results in fast execution times,
    even on large data sets, and does not require knowledge of the phylogenetic
    relationships among sequences. In a test case on a primate pseudogene, the
    matrix we arrived at resembles one obtained using maximum likelihood, and
    the resulting distance measure is shown to have better linearity than is
    obtained in a less general model.