ETE tools

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.

Index of tools

  • ete build: Build gene and species trees with a single command.

    ete3 build -a seqs.fasta -w soft_modeltest -o mytree/

  • ete evol: Run and visualize CodeML and SLR analyses.

    ete3 evol -t tree.nw --alg alg.fasta --models b_neut b_free --mark branchName -o test/

  • ete compare: Calculate distances between trees.

    ete3 compare -t tree1.nw -r tree2.nw

  • ete ncbiquery: Run fast inline queries to the NCBI taxonomy database.

    ete3 ncbiquery --search 9606 Hominidae "Canis familiaris" --info

  • ete view: Visualize and generate tree images

    ete3 view -t tree.nw

  • ete annotate: annotate tree nodes with external data or using NCBI taxonomy information.

    ete3 annotated -t tree.nw --ncbi

  • ete mod: manipulate tree topology by rooting, pruning or sorting branches.

  • ete maptrees: (experimental)

all ETE tools can be combined with other Unix commands by using pipes