Figure 1.

Tree visualization. An example tree with the code to generate each plot shown below each plot. First, a phyloXML tree of the Apaf-1 protein family [27] is downloaded, read by Bio.Phylo, and plotted with default settings. The tree is then rerooted at the midpoint of its two most divergent tips and ladderized such that sibling clades with a larger number of descendents are listed first. The clade of genes belonging to vertebrate species is identified as the common ancestor of the human and zebrafish, after inspection of the original tree. The vertebrate clade is highlighted with the color fuchsia and an increased branch width, and the rest of the tree is colored gray. Finally, the tree is plotted again

Talevich et al. BMC Bioinformatics 2012 13:209   doi:10.1186/1471-2105-13-209
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