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<title>Overview</title>
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<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Packages table, listing packages, and an explanation">
<caption><span>Packages</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
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<td class="colFirst"><a href="pal/algorithmics/package-summary.html">pal.algorithmics</a></td>
<td class="colLast"> </td>
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<td class="colFirst"><a href="pal/alignment/package-summary.html">pal.alignment</a></td>
<td class="colLast">
<div class="block">Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.</div>
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<tr class="altColor">
<td class="colFirst"><a href="pal/coalescent/package-summary.html">pal.coalescent</a></td>
<td class="colLast">
<div class="block">Classes to model population genetic processes using the coalescent.</div>
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<td class="colFirst"><a href="pal/datatype/package-summary.html">pal.datatype</a></td>
<td class="colLast">
<div class="block">Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)</div>
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<td class="colFirst"><a href="pal/distance/package-summary.html">pal.distance</a></td>
<td class="colLast">
<div class="block">Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="pal/eval/package-summary.html">pal.eval</a></td>
<td class="colLast">
<div class="block">Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.</div>
</td>
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<tr class="altColor">
<td class="colFirst"><a href="pal/gui/package-summary.html">pal.gui</a></td>
<td class="colLast">
<div class="block">GUI components for some special objects (e.g., trees).</div>
</td>
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<td class="colFirst"><a href="pal/io/package-summary.html">pal.io</a></td>
<td class="colLast">
<div class="block">Classes for simple (formatted) input/output from/to files,
strings and standard-in/out streams.</div>
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<td class="colFirst"><a href="pal/math/package-summary.html">pal.math</a></td>
<td class="colLast">
<div class="block">Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.</div>
</td>
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<td class="colFirst"><a href="pal/mep/package-summary.html">pal.mep</a></td>
<td class="colLast">
<div class="block">Classes for the analysis of "measurably evolving populations" (mep).</div>
</td>
</tr>
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<td class="colFirst"><a href="pal/misc/package-summary.html">pal.misc</a></td>
<td class="colLast">
<div class="block">Classes that don't fit elsewhere ;^)</div>
</td>
</tr>
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<td class="colFirst"><a href="pal/popgen/package-summary.html">pal.popgen</a></td>
<td class="colLast">
<div class="block">Classes for providing 'classical' population genetics analyses.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="pal/statistics/package-summary.html">pal.statistics</a></td>
<td class="colLast">
<div class="block">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.)</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="pal/substmodel/package-summary.html">pal.substmodel</a></td>
<td class="colLast">
<div class="block">Classes describing substitution models, i.e.</div>
</td>
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<td class="colFirst"><a href="pal/supgma/package-summary.html">pal.supgma</a></td>
<td class="colLast"> </td>
</tr>
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<td class="colFirst"><a href="pal/tree/package-summary.html">pal.tree</a></td>
<td class="colLast">
<div class="block">Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="pal/treesearch/package-summary.html">pal.treesearch</a></td>
<td class="colLast"> </td>
</tr>
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<td class="colFirst"><a href="pal/util/package-summary.html">pal.util</a></td>
<td class="colLast">
<div class="block">Utility classes for sorting etc.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="pal/xml/package-summary.html">pal.xml</a></td>
<td class="colLast">
<div class="block">Utility classes for converting PAL objects to and from XML documents.</div>
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