Table 1

Summary of ETE's features

Module

Description


General trees

Advanced node annotation, tree topology manipulation, automatic tree pruning, cut & paste partitions, trees concatenation, random trees generation, iterate over leaves and descendants, pre and pos-order tree traversal, rooting options, advanced nodes search, get distances among nodes, detect midpoint outgroup, find farthest descendant node, find farthest node in the whole tree, detect first common ancestor among nodes, text mode visualization, newick rendering (several formats), extended newick format integration, built-in python operations: print, len, iter, in.


Phylogenetic trees

Link to multiple sequence alignments, automatic species name detection, check node monophyly, evolutionary events dating, detect orthology and paralogy relationships: species overlap and tree reconciliation methods, complete access API to the phylomeDB database, integrated visualization (show molecular sequences and evolutionary events).


Clustering trees

link to numerical matrices, calculate inter and intra-cluster distances among clusters, calculate Silhouette and Dunn Indexes, integrated visualization (display numerical profiles in several formats).


Tree Visualization

Interactive Graphical User Interface, programmable drawing engine, independent node aspect editing, support drawing node extra features (text or external images), vector graphics rendering using PDF format.


Huerta-Cepas et al. BMC Bioinformatics 2010 11:24   doi:10.1186/1471-2105-11-24

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