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 TypeClassDescriptionclassgenerates bootstrapped alignments from a raw alignmentclassconcatenates a list of alignments to one single alignment, increasing the number of sitesclassThis is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.classCreates a "Gap-Balanced" alignment.classThis class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.classan extension of the IndelAlignment that includes annotation.classgenerates jumbled alignments (randomizing input order of sequences)classMultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.classreads aligned sequence data from plain text files.classreads aligned sequence data from plain text files.classAn alignment class that can be efficiently constructed from an array of strings.classThis is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.classtakes an Alignment and determines its site patternsclasstakes an alignment and repeatedly removes sitesclassThis 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