Package | Description |
---|---|
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).
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
SimulatedAlignment
generates an artificial data set
|