ETE-tools: a collection of command line tools to manipulate, analyze, visualize and build phylogenetic trees

The ETE toolkit offers a collection of command line tools to run common operations in phylogenetics and comparative genomics. All tools are wrapped by the ete3 command, which will become available after ETE installation.
ete build: Build gene and species trees with a single command.
ete evol: Run and visualize CodeML and SLR analyses.
ete compare: Calculate distances between trees.
ete ncbiquery: Run fast inline queries to the NCBI taxonomy database.
ete view: Visualize and generate tree images
ete annotate: annotate tree nodes with external data or using NCBI taxonomy information.
ete mod: manipulate tree topology by rooting, pruning or sorting branches.
all ETE tools can be combined with other Unix commands by using pipes
ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046