Gene tree coloring

Answer: 

Taxonomic-based Coloring

By default, gene trees in the genome browser are colored according to taxonomic level. For example, genes from Anopheline mosquitos will have a pink background, and genes from sandflies will have a yellow background. The coloring can be switched off, or configured so that the text is colored (on a white background). To configure the coloring, from a gene tree page select Configure this page from the menu on the left, and set the Colour tree according to taxonomy option to either "No colouring", "Background", or "Foreground".

The taxonomic levels and colors are:

  • Anophelinae: pink
  • Culicinae: orange
  • Phlebotominae: yellow
  • Brachycera: turquoise
  • Hemiptera: blue
  • Phthiraptera: blue
  • Chelicerata: blue
  • Gastropoda: purple

If sub-trees are collapsed in the gene tree display, these will be colored if the sub-tree contains only species from one taxonomic level. Note that Drosophila melanogaster, which is included in our comparative analyses despite not being a "VectorBase species", always has a white background.

The following example shows the default taxonomic coloring:
Taxonomic-based coloring

Highlighting Annotations

Layered on top of the taxonomic coloring, it is also possible to highlight (with a green background around the ID) genes which are attached to a chosen GO or InterPro term. These can be selected in the Annotations table above the gene tree display. Note that a collapsed sub-tree in the gene tree display will be highlighted if any (not necesarily all) genes within the sub-tree are annotated with the term.

The next example shows 'foreground' taxonomic coloring, with highlighting on the genes that have been annotated with the SH3 InterPro domain:
Highlighting annotations