https://github.com/agormp/treedist
Computes measures of (dis)similarity between phylogenetic trees. Provides summaries of shared and unique bipartitions.
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Computes measures of (dis)similarity between phylogenetic trees. Provides summaries of shared and unique bipartitions.
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README.md
treedist
The command-line program treedist takes as input two or more treefiles and computes various measures of the "distance" between pairs of trees. The program can also output information about how many and what bipartitions differ between trees.
Availability
The treedist source code is available on GitHub: https://github.com/agormp/treedist. The executable can be installed from PyPI: https://pypi.org/project/treedist/
Installation
python3 -m pip install treedist
Dependencies
treedist relies on the phylotreelib library, which is automatically included when using pip to install.
Overview
- Input:
- Two or more files containing phylogenetic trees in NEXUS or Newick format
- Trees do not need to have identical leaves, but each pair of trees need to share at least 4 leaves (all leaves that are not shared will be automatically pruned before computing tree distances).
- Output:
- Different measures of treesimilarity (Robinson-Foulds symmetric distance, normalised RF, normalised similarity)
- Summaries of what bipartitions that differ or are shared between trees
Usage
``` Usage: treedist [options] TREEFILE1 TREEFILE2 [TREEFILE3 ...]
Options: --version show program's version number and exit -h, --help show this help message and exit -I FORM, --informat=FORM format of tree files: NEXUS or newick [default: newick] -d, --symnormdist print normalized symmetric distance -s, --symdist print symmetric distance -b, --bipnumbers print no. total, shared, and unique bipartitions for each tree -u, --uniquelist print list of unique bipartitions for each tree -c, --commonlist print list of bipartitions trees have in common -l, --labels also print branch labels for bipartitions (requires -c or -u) -o, --oneline oneline output of normalized symmetric similarities -n, --namesummary Print names of leaves that are shared between trees, and leaves that are discarded --collapselen=BRLEN[,BRLEN,...] Collapse branches shorter than this (comma-separated list: individual cutoffs for trees) --collapsefrac=FRAC Collapse branches shorter than FRAC fraction of treeheight (of minimum variance rooted tree) --collapsesupport=SUPPORT Collapse branches with less clade support than this (must be number in [0,1]) ```
Usage examples
TBD
Owner
- Name: Anders Gorm Pedersen
- Login: agormp
- Kind: user
- Location: Denmark
- Company: Technical University of Denmark
- Repositories: 9
- Profile: https://github.com/agormp
Professor of Bioinformatics
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pypi.org: treedist
Computes measures of (dis)similarity between phylogenetic trees. Provides summaries of shared and unique bipartitions.
- Homepage: https://github.com/agormp/treedist
- Documentation: https://treedist.readthedocs.io/
- License: GNU General Public License v3 (GPLv3)
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Latest release: 1.0.1
published over 3 years ago