PhyloTraits
PhyloTraits is a Julia package with core utilities for phylogenetic networks. See the PhyloNetworks package, which PhyloTraits depends on, for background on phylogenetic networks and for how to get help.
References
See them in bibtex format.
Quick links for methods about trait evolution on networks:
- Teo, Rose, Bastide & Ané (2023). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. Bulletin of the Society of Systematic Biologists, 2(3):1-29. doi: 10.18061/bssb.v2i3.8977
- Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi:10.1093/sysbio/syz073.
- Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018). Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5):800–820. doi:10.1093/sysbio/syy033.
Manual
The manual pages contain detailed tutorials on how to use the functions of the package.
- Continuous trait analysis
- Continuous trait simulation
- Discrete trait evolution
- fitting DNA substitution parameters on a network
- Discrete trait simulation
Examples
This section contains example of empirical analyses from the literature.
Library
For help on individual functions, see this library.