PartList is a simple command-line tool that lists the partitions and corresponding edge lengths for each edge in a given phylogenetic tree.
- Parses a Newick-formatted tree
- Outputs a table showing each bipartition (split) and its edge length
- Outputs partitions in lexicographical order for consistency
To compile the program, use:
g++ partlist.cpp -o partlist./partlist [tree_file]tree_file: A text file containing a tree in Newick format.
Input file: example.treefile
(protopterus:0.3099067061,((python:0.0963168749,(Taeniopygia:0.0641893111,(caiman:0.0134032165,(caretta:0.0105108952,phrynops:0.0269820819):0.0371040668):0.0204716388):0.0144828411):0.0360088912,Ornithorhynchus:0.1286353020):0.0905913632,Xenopus:0.3075276653);
Command:
./partlist example.treefileOutput:
| Partition | Edge length |
|---|---|
| Ornithorhynchus,Taeniopygia,Xenopus,caiman,caretta,phrynops,protopterus::python | 0.096317 |
| Ornithorhynchus,Taeniopygia,Xenopus,caiman,caretta,phrynops,python::protopterus | 0.309907 |
| Ornithorhynchus,Taeniopygia,Xenopus,caiman,caretta,protopterus,python::phrynops | 0.026982 |
| Ornithorhynchus,Taeniopygia,Xenopus,caiman,phrynops,protopterus,python::caretta | 0.010511 |
| Ornithorhynchus,Taeniopygia,Xenopus,caiman,protopterus,python::caretta,phrynops | 0.037104 |
| Ornithorhynchus,Taeniopygia,Xenopus,caretta,phrynops,protopterus,python::caiman | 0.013403 |
| ... (remaining rows omitted for clarity) ... |
Each row represents a bipartition induced by an internal edge of the tree, with the two sets of taxa separated by ::.
This project is released under the MIT License.