Uses of Class
pal.alignment.AbstractAlignment

Packages that use AbstractAlignment
pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating. 
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). 
 

Uses of AbstractAlignment in pal.alignment
 

Subclasses of AbstractAlignment in pal.alignment
 class BootstrappedAlignment
          generates bootstrapped alignments from a raw alignment
 class ConcatenatedAlignment
          concatenates a list of alignments to one single alignment, increasing the number of sites
 class ConcatenatedAnnotatedAlignment
          This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
 class GapBalancedAlignment
          Creates a "Gap-Balanced" alignment.
 class IndelAlignment
          This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
 class IndelAnnotatedAlignment
          an extension of the IndelAlignment that includes annotation.
 class JumbledAlignment
          generates jumbled alignments (randomizing input order of sequences)
 class MultiLocusAnnotatedAlignment
          MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
 class ReadAlignment
          reads aligned sequence data from plain text files.
 class ReadAlignmentOld
          reads aligned sequence data from plain text files.
 class SimpleAlignment
          An alignment class that can be efficiently constructed from an array of strings.
 class SimpleAnnotatedAlignment
          This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
 class SitePattern
          takes an Alignment and determines its site patterns
 class StrippedAlignment
          takes an alignment and repeatedly removes sites
 class StrippedAnnotatedAlignment
          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
 class SimulatedAlignment
          generates an artificial data set