Branch lengths of the ML tree were optimized for each gene partition and the variance-covariance matrix of evolutionary rates was estimated using Estbranches.
MatrixConverter can output discrete character matrices for phylogenetic or other evolutionary analyses, such as tests for phylogenetic signal, ancestral state reconstructions, or tests to relate phenotypic characters with diversification, in NEXUS (Maddison et al., 1997), PHYLIP, or NeXML format (Vos et al., 2012), or as a text file.
Evolutionary distance matrices for the neighbour-joining/UPGMA method were computed using the DNADIST algorithm program.
Pairwise evolutionary distance matrices for concatenated alignments of exons or introns from human and mouse linc RNA genes were calculated using the DNADIST program from the PHYLIP package (Felsenstein 1996), with the Kimura nucleotide substitution model.
Robustness of these phylogenies was evaluated by two additional programs, PHYML (maximum likelihood analysis) [ 45] and MrBayes (Bayesian estimation of phylogeny) [ 46] with different parameters (for example, transition matrices and evolutionary models).
Compare with the random circuit matrix method, our approach uses less code length for evolutionary hardware description.
In this article, the McLachlan chemical similarity matrix (McLachlan, 1972) and BLOSUM45 substitution matrix (Henikoff and Henikoff, 1992) were used for chemical similarity and for evolutionary correlation, respectively.
SplitsTree (www.splitstree.org) was used for evolutionary tree construction by decomposition analyses using the distance matrix produced from pairwise comparisons of concatenated sequences to determine interconnected networks (28 ).
The 'common principal component' approach and resulting hierarchy of models have seen considerable use in the comparison of covariance matrices in evolutionary biology; see Houle et al. [ 41] for a discussion.
