Category | Method | Reference |
---|---|---|
I/O | Tree (NEWICK) Sequences (FASTA, PHYLIP) Protein Structure (PDB) | Â |
Tree manipulation | Random/exhaustive: Subtree Pruning Regrafting (SPR) Tree Bissection Reconnection (TBR) Nearest Neighbor interchange (NNI) Branch Swapping Stepwise addition | [7] |
Phylogeny | Neighbor Joining | [8] |
 | Greedy Majority-rule consensus | [9] |
 | Maximum Likelihood Rates across site modeling Estimation of shape parameter α | [10] |
ML confidence intervals | KH | [11] |
 | SH | [12] |
 | RELL | [13] |
 | Expected Likelihood Weights | [14] |
ML performance | P-matrix caching Chebyshev Polynomial approximation | [15] |
Substitution matrices | JTT | [16] |
 | PAM | [17] |
 | WAG | [18] |
Simulation | Protein Sequence Simulation (Rates across sites, rate shifts, site specific frequencies, multiple datasets, likelihood computation) | [5, 19] |
 | Random Number generation | [20] Acknowl. Z. Yang for implementation in PAML |
Structural Biology | Manipulation / mapping Neighboring site anisotropy (NSA) Geometric transformations Distance/Contact Matrices | [6] |