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| Packages that use pal.util | |
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| pal.algorithmics | |
| pal.alignment | Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating. |
| pal.coalescent | Classes to model population genetic processes using the coalescent. |
| pal.distance | Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances). |
| pal.misc | Classes that don't fit elsewhere ;^) |
| pal.statistics | Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.) |
| pal.substmodel | Classes describing substitution models, i.e. |
| pal.supgma | |
| pal.tree | Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). |
| pal.treesearch | |
| pal.util | Utility classes for sorting etc. |
| pal.xml | Utility classes for converting PAL objects to and from XML documents. |
| Classes in pal.util used by pal.algorithmics | |
|---|---|
| AlgorithmCallback
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| Classes in pal.util used by pal.alignment | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.coalescent | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.distance | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.misc | |
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| Comparable
interface for an object that is comparable. |
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| Classes in pal.util used by pal.statistics | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.substmodel | |
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| DoubleKeyCache
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| XMLConstants
constants (strings and numbers) relating to reading and writing XML. |
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| Classes in pal.util used by pal.supgma | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.tree | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.treesearch | |
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| AlgorithmCallback
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| Classes in pal.util used by pal.util | |
|---|---|
| AlgorithmCallback
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| Comparable
interface for an object that is comparable. |
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| Comparator
interface for an object that can compare other objects for the purposes of ordering them. |
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| DoubleKey
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| DoubleKeyCache
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| Logger
Interface for all objects that provide a logging facility. |
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| Classes in pal.util used by pal.xml | |
|---|---|
| XMLConstants
constants (strings and numbers) relating to reading and writing XML. |
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