TCGenerators
TCGenerators is a Python software tool that generates all possible binary tree-child (BTC) networks with a given number of leaves. BTC networks are a subclass of phylogenetic networks that generalize phylogenetic trees by allowing the modeling of reticulate evolution events.
The tool uses recursive reduction/augmentation operations to efficiently generate these networks, extending and generalizing similar operations for phylogenetic trees. These operations are biologically relevant and can also be used to extend the evolutionary history of a set of sequences represented by a BTC network to include a new sequence. The recursive nature of the solution provides an upper bound on the number of such networks through a recurrence relation.
Topic
Phylogenetics;Molecular interactions, pathways and networks
Detail
Operation: Phylogenetic tree generation (consensus);Phylogenetic tree bootstrapping;Phylogenetic tree reconstruction
Software interface: Command-line user interface
Language: Python
License: Not stated
Cost: Free of charge
Version name: -
Credit: Spanish Ministry of Science, Innovation and Universities, European Regional Development Fund.
Input: -
Output: -
Contact: Gabriel Cardona gabriel.cardona@uib.es
Collection: -
Maturity: -
Publications
- Generation of Binary Tree-Child phylogenetic networks.
- Cardona G, et al. Generation of Binary Tree-Child phylogenetic networks. Generation of Binary Tree-Child phylogenetic networks. 2019; 15:e1007347. doi: 10.1371/journal.pcbi.1007347
- https://doi.org/10.1371/JOURNAL.PCBI.1007347
- PMID: 31509525
- PMC: PMC6756559
Download and documentation
Documentation: https://github.com/bielcardona/TCGenerators/blob/master/README.md
Home page: https://github.com/bielcardona/TCGenerators
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