Package pal.alignment

Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.

See:
          Description

Interface Summary
Alignment interface for any alignment data.
AnnotationAlignment The AnnotationAlignment interface is designed to provide annotation for an alignment.
CharacterAlignment This interface is designed to hold quantitative character states.
 

Class Summary
AbstractAlignment abstract base class for any alignment data.
AlignmentUtils Helper utilities for alignments.
AminoAcidAlignment generates an amino acid alignment from a nucleotide alignment.
BootstrappedAlignment generates bootstrapped alignments from a raw alignment
CodonAlignment generates an codon alignment from a nucleotide alignment.
ConcatenatedAlignment concatenates a list of alignments to one single alignment, increasing the number of sites
ConcatenatedAnnotatedAlignment This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
GapBalancedAlignment Creates a "Gap-Balanced" alignment.
Genotype This class provides from genotype to be constructed from separate but paired alignments.
IndelAlignment This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
IndelAnnotatedAlignment an extension of the IndelAlignment that includes annotation.
JumbledAlignment generates jumbled alignments (randomizing input order of sequences)
MultiLocusAnnotatedAlignment MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
ReadAlignment reads aligned sequence data from plain text files. recognizes PHYLIP 3.4 INTERLEAVED, PHYLIP SEQUENTIAL, CLUSTAL and derived formats. Other features: - the dot as "copy character" is recognized, - all base characters are capitalized, - automatic data type estimation - determination of corresponding base frequencies.
SimpleAlignment An alignment class that can be efficiently constructed from an array of strings.
SimpleAnnotatedAlignment This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
SimpleCharacterAlignment This provides a basic implementation of CharacterAlignment.
SitePattern takes an Alignment and determines its site patterns
StrippedAlignment takes an alignment and repeatedly removes sites
StrippedAnnotatedAlignment This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.
 

Exception Summary
AlignmentParseException Exception thrown by ReadAlignment
 

Package pal.alignment Description

Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.