Uses of Class
statalign.model.subst.SubstitutionModel

Packages that use SubstitutionModel

statalign.base
statalign.model.ext
statalign.model.ext.plugins
statalign.model.subst
statalign.model.subst.plugins
statalign.postprocess.gui

Uses of SubstitutionModel in statalign.base

Fields in statalign.base declared as SubstitutionModel

SubstitutionModel	InputData.model The current substitution model that is used to analyse the sequences.
SubstitutionModel	Tree.substitutionModel Characters on this tree undergo substitutions according to this model.

Methods in statalign.base with parameters of type SubstitutionModel

void	TreeAlgo.addAlignSeqsToTree(Tree tree, java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)
Tree	TreeAlgo.buildNJTree(java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)

Uses of SubstitutionModel in statalign.model.ext

Methods in statalign.model.ext with parameters of type SubstitutionModel

void	ModelExtManager.afterSubstParamChange(Tree tree, SubstitutionModel model, int ind, boolean accepted)
void	ModelExtension.afterSubstParamChange(Tree tree, SubstitutionModel model, int ind, boolean accepted) Called after a proposed indel parameter change (accepted or rejected).
void	ModelExtManager.beforeSubstParamChange(Tree tree, SubstitutionModel model, int ind)
void	ModelExtension.beforeSubstParamChange(Tree tree, SubstitutionModel model, int ind) Called before a substitution parameter change is proposed.
double	ModelExtManager.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind) Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.
double	ModelExtension.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind)

Uses of SubstitutionModel in statalign.model.ext.plugins

Methods in statalign.model.ext.plugins with parameters of type SubstitutionModel

double

StructAlign.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind)

Uses of SubstitutionModel in statalign.model.subst

Method parameters in statalign.model.subst with type arguments of type SubstitutionModel

static java.lang.String	SubstitutionModel.getMenuName(java.lang.Class<? extends SubstitutionModel> cl) Retrieves menuName static field of a SubstitutionModel plug-in class.
static java.lang.String	SubstitutionModel.getType(java.lang.Class<? extends SubstitutionModel> cl) Retrieves the static field type of a SubstitutionModel plug-in class.

Uses of SubstitutionModel in statalign.model.subst.plugins

Subclasses of SubstitutionModel in statalign.model.subst.plugins

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

Uses of SubstitutionModel in statalign.postprocess.gui

Constructors in statalign.postprocess.gui with parameters of type SubstitutionModel

AlignmentGUI(java.lang.String title, SubstitutionModel subst)
It initializes a new panel for alignments.

AlignmentGUI(java.lang.String title, SubstitutionModel subst, Postprocess _owner)
It initializes a new panel for alignments.