From: Parameterizing sequence alignment with an explicit evolutionary model
Microscopic model | Macroscopic model | ||||
---|---|---|---|---|---|
Evolutionary model | Total # free parameters | Rates | Geometric parameters | # States minimal pair HMM | Other properties |
Single-residue models(Fig. 2, Additional file 1: Figure S1 and S2) | |||||
aali | 6 | \(\lambda,\mu,\mu _{A}^{\{\text {\textit {M,D,I}}\}}\) | p | 3 | affine ancestral residues; linear inserts |
li | 4 | λ,μ,μ A | p | 1 | linear; particular case of aali |
lr | 2 | λ,μ A ,(μ=λ+μ A ) | (p lr=λ/μ A ) | 1 | reversible; particular case of li |
tkf91 | 2 | λ,μ | (p tkf=λ/μ) | 2 | quasi linear; [5] |
afg | 9 | \(\lambda,\mu,\mu _{A}^{\{\text {\textit {M,D,I}}\}}\) | r M ,r D ,r I ,p | 3 | fragment-derivative of aali |
afr | 4 | λ,μ A ,(μ=λ+μ A ) | r M ,r D =r I ,(p lr) | 3 | reversible; compatible with Smith-Waterman |
tkf92 | 3 | λ,μ | r, (p tkf92) | 3 | fragment-derivative of tkf91; [6] |
Compatible with profile HMMs(Fig. 5) | |||||
aif | 7 | \(\lambda,\mu,\mu _{A}^{\{\text {\textit {M,D,I}}\}}\) | r I ,p | 3 | inserts-only fragment-derivative of aali |
aga | 7 | \(\lambda,\mu,\mu _{A}^{\{\text {\textit {M,D,I}}\}}\) | s I ,p | 3 | time-independent geometric inserts |