Uses of Class
pal.alignment.AbstractAlignment
Packages that use AbstractAlignment
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Uses of AbstractAlignment in pal.alignment
Subclasses of AbstractAlignment in pal.alignmentModifier and TypeClassDescriptionclass
generates bootstrapped alignments from a raw alignmentclass
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.class
Creates a "Gap-Balanced" alignment.class
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.class
an extension of the IndelAlignment that includes annotation.class
generates jumbled alignments (randomizing input order of sequences)class
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.class
reads aligned sequence data from plain text files.class
reads aligned sequence data from plain text files.class
An alignment class that can be efficiently constructed from an array of strings.class
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.class
takes an Alignment and determines its site patternsclass
takes an alignment and repeatedly removes sitesclass
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments. -
Uses of AbstractAlignment in pal.tree
Subclasses of AbstractAlignment in pal.tree