Constructs the FLU substitution matrix for amino acid changes, based on data from the FLU model developed by Dang et al. (2010). The FLU model is specifically tuned for influenza protein evolution and is formatted in PAML/PhyML-style: the lower triangle of the rate matrix followed by equilibrium frequencies.
Value
A 20x20 numeric matrix representing the FLU amino acid substitution rates, with amino acids ordered alphabetically by their one-letter codes.
Details
This function hardcodes the substitution matrix values from the original dataset provided by Dang et al. (2010) to avoid repeated file I/O during usage. The final matrix is symmetric and suitable for phylogenetic and protein evolution analyses using the FLU model.
References
- Dang, C.C., Le, Q.S., Gascuel, O., & Le, V.S. (2010). FLU, an amino acid substitution model for influenza proteins. *BMC Evolutionary Biology*, 10, 99. doi:10.1186/1471-2148-10-99 - Source file available from: ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU