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Packages that use AbstractAlignment | |
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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 |
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Subclasses of AbstractAlignment in pal.alignment | |
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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 |
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Subclasses of AbstractAlignment in pal.tree | |
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class |
SimulatedAlignment
generates an artificial data set |
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