Gene/protein tree

Answer: 

VectorBase gene trees are generated by the Gene Orthology/Paralogy prediction method pipeline. All homologues are determined from gene trees.

Gene trees are constructed using one representative protein for every gene in every species. (They can also be considered as protein trees).

The display shows the maximum likelihood phylogenetic tree representing the evolutionary history of genes. These trees are reconciled with a species tree, generated by TreeBeST. Internal nodes are then annotated for duplication (red boxes) or speciation (blue boxes) events.

Red squares represent duplications nodes, blue squares represent speciation nodes, giving rise to paralogues and orthologues. Another class of node, ambiguous, is shown as a lighter blue square.

The gene of interest is highlighted in red and within-species paralogues are shown in blue, if the option to view paralogues is selected (below the tree diagram).

Taxonomy IDs refer to the NCBI Taxonomy Browser.The number at the top of pop-up menus (upon clicking on a node) corresponds to the node_id from the protein_tree_node table in the compara database.

Multiple alignment of the peptides (green bars) was made using MUSCLE. Green bars shows areas of amino acid alignment, white areas are gaps in the alignment. Dark green bars indicate consensus alignments.

Click on a node to expand a collapsed set of branches into a full tree. The consensus amino acid alignment corresponds to the consensus residues in the collapsed node, and will be expanded when the tree is expanded.

Configure this page to customise the tree. Colouring by clade can be removed.