Additional file 14.
Maximum-likelihood tree of SRA proteins.Caenorhabditis elegans names are green, C. briggsae names are blue, and C. remanei names are red. Species-specific clades are emphasized by having their branch lines match the species color. The smaller inset is the same tree with names removed, which shows the tree structure more clearly. Open circles on branches indicate a branch support value of 0.9 or higher, as computed by phyml-alrt. Strict ortholog trios (1-1-1) are marked with a filled black square. The tree was rooted by inclusion of a sampling of SRAB proteins (not shown). The scale bar indicates number of amino acid changes per site in the large tree. Each name includes a species identifier, gene identifiers, and genome start and end coordinates for the corresponding gene model. The C. elegans gene names include both a standard genome project name (for example, F28C12.3) and a genetic gene name (for example, sra-19). The C. briggsae gene name is the brigpep WormBase name when applicable (for example, CBG04324) or an arbitrarily numbered GeneWise prediction number (for example, gw15). The C. remanei names are either the WormBase wum gene prediction (for example, wum.4.1), the WormBase genefinder prediction (for example, gf170), or an arbitrarily numbered GeneWise prediction number (for example, gw16). The wum or gf names combined with the supercontig number uniquely identify the prediction in the current C. remanei prediction set on WormBase. The sequences analyzed are given in Additional files 11 to 13. All trees are available in Newick format upon request.
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Thomas and Robertson BMC Biology 2008 6:42 doi:10.1186/1741-7007-6-42