A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

J

JAVADOCS - Static variable in class statalign.ui.MainFrame

joins - Variable in class statalign.postprocess.plugins.contree.CNetworkNode

joinStrings(Object[], String) - Static method in class statalign.base.Utils

Joins strings using a separator string.

joinStrings(Object[], String, String) - Static method in class statalign.base.Utils

Joins strings using a prefix and a separator string.

Jones - Class in statalign.model.subst.plugins

Implements the JTT (Jones-Taylor-Thornton) substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/1633570

Jones() - Constructor for class statalign.model.subst.plugins.Jones

Constructor used when instantiation is necessary.

JukesCantor - Class in statalign.model.subst.plugins

Implements the Jukes-Cantor model for nucleic acids.

JukesCantor() - Constructor for class statalign.model.subst.plugins.JukesCantor

This constructor reads transition rates from the file data/jukescantor_rate.dat, the alphabet from data/DNAalphabet.dat, and the equilibrium distribution from data/jukescantor_equilibrium.dat.