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Example sentences for: least-square
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Phylogenetic trees were constructed by first generating a distance matrix using the PROTDIST program and the Dayhoff PAM model for amino-acid substitutions and employing this matrix for minimum evolution (least-square) tree building [ 30] using the FITCH program.
Pairwise evolutionary distances between the sequences in concatenated alignments were calculated using the Dayhoff PAM model as implemented in the PROTDIST program of the PHYLIP package [ 44 ] . A distance tree was constructed from the resulting distance matrix by using the least-square [ 46 ] method as implemented in the FITCH program of PHYLIP [ 44 ] . The maximum likelihood tree was constructed with the JTT-F model of amino acid substitutions [ 47 ] , as implemented in the ProtML program of the MOLPHY package [ 48 ] , by optimizing the least squares tree with local rearrangements.
Given the 100 genes selected, methods such as principal component analysis, partial least-square regression or composite covariate predictor can be used to further reduce the gene dimension to two or three dimensions by taking linear combinations of the gene expression levels.
This prediction is not supported by linear least-square regressions, which fail to detect any substantial differences in the correlation between K s and codon bias in paralogous versus orthologous genes (data not shown), suggesting that the observation of a higher K n /K s ratio in paralogous genes cannot be explained by an underestimate of synonymous divergence in paralogs.
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