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