ETE Toolkit 4

Scope

Use ETE 4 to work with an existing tree:

• Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write Newick trees
• Compare topologies and calculate phylogenetic distances
• Find repeated subtree topologies with TreePattern
• Analyze gene trees with PhyloTree
• Query local NCBI or GTDB taxonomy databases
• Explore large trees interactively with SmartView
• Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview

ETE does not replace sequence alignment or phylogenetic inference software. For raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or another inference tool; then load the resulting tree into ETE.