Table 1.

A Summary of Analyses and Substitution Models in MEGA5

Sequence alignments

DNA, codon, and protein alignments; both manual and automated alignments with trace file Editor. Built-in automated aligners: CLUSTALW  and MUSCLE*.

Major analyses (statistical approach in parentheses)

Models and parameters: Select Best-Fit Substitution Model* (ML); test pattern homogeneity; Estimate Substitution Pattern (MCL, ML*);  Estimate Rate Variation Among Sites* (ML); Estimate Transition/Transversion Bias (MCL, ML*); Estimate Site-by-Site Rates* (ML).

Infer phylogenies: Infer Phylogenetic Trees (NJ, ML*, ME, MP); Phylogeny Tests (Bootstrap and Branch-length tests); Branch-and-Bound Exact  Search (MP); Heuristic Searches: Nearest-Neighbor-Interchange (NNI; ML*, ME, MP), Close-Neighbor-Interchange (CNI; ML*, ME, MP), and  Max–Mini (MP)

Compute distances: Pairwise and Diversity; Within- and Between-Group Distances; Bootstrap and Analytical Variances; separate distances by  Site Degeneracy, Codon Sites; Separation of Distances in Transitions and Transversions; Separate Nonsynonymous and Synonymous Changes

Tests of Selection: For Complete Sequences or Set of Codons; Sequence Pairs or Groups (Within and Between)

Ancestral Sequences: Infer by ML with Relative Probabilities for bases or residues* or by MP (all parsimonious pathways)

Molecular Clocks: Tajima’s 3-Sequence Clock Test*; Likelihood Ratio Test (ML) for a Topology*; Estimate Branch Lengths under Clock*

Substitution models (+F = with empirical frequencies; REV = reversible)

DNA: General Time Reversible (GTR)*, Tamura–Nei, Hasegawa–Kishino–Yano*, Tamura Three-Parameter, Kimura Two-Parameter, Tajima– Nei, Jukes–Cantor

Codons: Nei–Gojobori (original and modified), Li–Wu–Lou (original and modified)

Protein: Poisson, Equal-Input, Dayhoff (+F), Jones–Taylor–Thornton (+F), Whelan and Goldman (+F)*, Mitochondrial REV (+F)*, Chloroplast  REV (+F)*, Reverse Transcriptase REV (+F)*

Rate Variation and Base Compositions: Gamma rates (G) and Invariant sites (I)* models; Incorporate Compositional Heterogeneity.

NOTE.—MCL, maximum composite likelihood; ME, minimum evolution; MP, maximum parsimony. An asterix (*) denotes features that are new in MEGA5.