csubst¶
Description¶
CSUBST is a tool for analyzing Combinatorial SUBSTitutions of codon sequences in phylogenetic trees.
Environment Modules¶
Run module spider csubst to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CSUBST_DIR - installation directory
- HPC_CSUBST_BIN - executable directory
Additional Usage Information¶
The main features of CSUBST include:
- Error-corrected rate of protein convergence with null expectation obtained by:
- Empirical or mechanistic codon substitution model
- Urn sampling from site-wise substitution frequencies (experimental)
- Flexible specification of "foreground" lineages and its comparison with - neighboring branches
- Heuristic detection of higher-order convergence involving more than two branches
- Simulated sequence evolution under specified scenarios of convergent evolution
- Convergent substitution mapping to protein structure
Citation¶
If you publish research that uses csubst you have to cite it as follows:
Fukushima K, Pollock DD. 2023. Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nature Ecology & Evolution 7: 155–170. http://doi.org/10.1038/s41559-022-01932-7
Categories¶
Biology, Phylogenetics