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Packages that use Alignments | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Ancestors | Provides classed to calculate ancestral reconstruction. |
Constraints | Provides classes to constrain the state of internal nodes. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Simulations | Provides a class to create simulate data. |
Classes in Alignments used by Alignments | |
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Alignment
Represents an "alignment", used very losely. |
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AlignmentException
Exception related to an alignment (currently only input errors) |
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Ambiguous
Stores details of ambiguous characters |
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Site
Represents a "site" in an "alignment". |
Classes in Alignments used by Ancestors | |
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Alignment
Represents an "alignment", used very losely. |
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AlignmentException
Exception related to an alignment (currently only input errors) |
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Site
Represents a "site" in an "alignment". |
Classes in Alignments used by Constraints | |
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Site
Represents a "site" in an "alignment". |
Classes in Alignments used by Likelihood | |
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Alignment
Represents an "alignment", used very losely. |
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Site
Represents a "site" in an "alignment". |
Classes in Alignments used by Simulations | |
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Alignment
Represents an "alignment", used very losely. |
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AlignmentException
Exception related to an alignment (currently only input errors) |
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Site
Represents a "site" in an "alignment". |
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