Package pal.alignment
package pal.alignment
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
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ClassDescriptionabstract base class for any alignment data.interface for any alignment data.A class for the gradual construction of an alignment.A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)Exception thrown by ReadAlignmentTemporary class for reading alignments...The SingleReceiver only keeps track of one alignment, the last one it receivedThe SingleReceiver only keeps track of one alignment, the last one it receivedSimple access for alignment functions.Helper utilities for alignments.The AnnotationAlignment interface is designed to provide annotation for an alignment.generates bootstrapped alignments from a raw alignmentThis interface is designed to hold quantitative character states.concatenates a list of alignments to one single alignment, increasing the number of sitesThis is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.Creates a "Gap-Balanced" alignment.This class provides from genotype to be constructed from separate but paired alignments.This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.an extension of the IndelAlignment that includes annotation.generates jumbled alignments (randomizing input order of sequences)MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.reads aligned sequence data from plain text files.reads aligned sequence data from plain text files.An alignment class that can be efficiently constructed from an array of strings.This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.This provides a basic implementation of CharacterAlignment.takes an Alignment and determines its site patternstakes an alignment and repeatedly removes sitesThis is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.