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.
|