Package statalign.model.subst.plugins

Class Summary

AminoAcidModel	Common superclass for amino acid substitution models.
Blosum	Implements the 'rate-matricized' Blosum substitution model.
CpRev	This class implements the Chloroplast reversible substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/10795826
Dayhoff	Implements the classic Dayhoff substitution model.
Felsenstein81	This class implements the Felsenstein 1981 parameter model.
Felsenstein84	This class implements the Felsenstein 1984 parameter model.
HKY85	This class implements the HKY85 parameter model.
Jones	Implements the JTT (Jones-Taylor-Thornton) substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/1633570
JukesCantor	Implements the Jukes-Cantor model for nucleic acids.
Kimura3	Implements the Kimura 3 parameter model.
MtMam	Implements the mammalian mitochondrial substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/9732458
MtREV	Implements the reversible mitochondrial substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/8642615
NucleotideModel	This is the abstract class for nucleotide models.
NucleotideModelUtils	This class implements various utility methods for nucleotide models.
ReversibleNucleotide	This class implements the general time reversible parameter model.
RtREV	Implements the retrovirus substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/12165843
Tamura92	This class implements the Tamura 1992 model.
TamuraNei	This class implements the Tamura-Nei parameter model.
Vt	Implements the Müller-Vingron substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/11382360
Wag	Implements the WAG (Whelan & Goldman model) substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/11319253