The ETE3-based script helping to extract names of neighbors from a phylogenetic tree. The script draws the phylogenetic tree with highlighted pivotal points (target leaves and MRCA of targets). The user can inspect the tree and remove non-neighbor leaves interactively. Use the 'Cut partition' command from the context menu to remove clades. After the ETE Tree Browser window is closed, the tree is saved and labels of the remained leaves are written.
pip install ete3
exnn_ete3.py [-h] tree targets neighbors
positional arguments:
tree Tree in the Newick format
targets Newline-separated target names
neighbors Newline-separated neighbor names (the output file)
Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction, analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi: 10.1093/molbev/msw046