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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
	<meta name="KeyWords"
			 content="PAL, phylogenetic analysis library, molecular phylogenetics,
					molecular evolution, phylogeny,
								tree reconstruction, maximum likelihood">
	<meta name="Content-Type" content="text/html; charset=iso-8859-1">
	<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
	<title>The PAL Project</title>
</head>
<body>

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									<a href = "index.html">About</a>
									<br>
									<a href = "people.html"> People Involved </a>
									<br>
									<b>Features</b>
									<br>
									<a href = "user_interfaces.html">User Interfaces</a>
									<br>
									<a href = "related.html">Related Projects</a>
									<br>
									<br>
									<a href = "download.html">Downloads and Installation</a>
									<br>
									<a href = "history.html">History</a>
									<br>
									<br>
									<a href = "contributing.html">Contributing</a>
									<br>
									<a href = "acknowledgements.html">Acknowledgements</a>
									<br>
									<br>
									<a href = "online.html">Pal Online</a>
								</td>
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<img src=pal.gif hspace=10 align=left ALT="PAL icon">
<strong><font size="+2">PAL: Phylogenetic Analysis Library</font></strong>

<br>
<br>
<strong><em>
<center>Main Features:</center>
</em></strong>
<p>
PAL is entirely written in the <a href="http://www.java.sun.com">Java language</a>.
This allows for a clean object oriented design while avoiding the complexities of C++.
Moreover, Java class code runs without needing recompilation on a wide range on
platforms.  Additionally, PAL also compiles into native code on Unix systems
(just like C++) using the
<a href="http://sourceware.cygnus.com/java/">GNU compiler for Java (gcj)</a>,
part of recent releases of the
<a href="http://gcc.gnu.org">GNU compiler collection (gcc)</a>.
Corresponding makefiles  are included with this distribution of PAL.
<P>
PAL consists of a rich variety of objects  to facilitate
the construction of special-purpose tools for phylogenetic analysis.
PAL contains, e.g., ready-to-use objects for:
<ul>

<li>
reading and writing sequence alignments, distance matrices, and trees
</li>

<li>
a large variety of substitution models for nucleotides and amino acids
(REV, TN, HKY, F84, F81, JC; Dayhoff, JTT, MTREV24, BLOSUM, VT, WAG, CPREV)
as well as for codons (Yang codon model)
</li>

<li>
Various models for rate variation over sites (invariable sites, Gamma)
</li>

<li>
efficient maximum-likelihood estimation  of pairwise  distances and
of branch lengths in a tree
(for unconstrained, clock, and dated-tips clock trees)
</li>

<li>
simulating coalescence intervals and estimation of demographic
parameters
</li>

<li>
likelihood ratio and chi-square tests and for
comparison of phylogenetic hypotheses
(e.g., Kishino-Hasegawa and Shimodaira-Hasegawa tests)
</li>

<li>
manipulating alignments (e.g., bootstrapping)
and trees and simulating data
</li>

<li>optimizing uni- and multivariate functions by various methods,
computing numerical derivatives, random numbers (simulation quality),
sorting etc.
</li>

<li>
creating formatted input and output from/to files,
standard io streams, and strings, through convenience classes that extend the
standard Java IO library
</li>

<li>
construct neighbor-joining, UPGMA and SUPGMA trees, and estimating least-squares
branch lengths on trees (weighted and unweighted LS)</li>

<li>translate nucleotide to AA sequences</li>

<li>access mathematical special functions (gamma, error, binomial)
and pdf, cdf, and quantile functions of statistical distributions
(gamma, exponential, chi-square, normal, Pareto)</li>

<li>
create split systems from trees and compute partition distances
between trees (Robinson-Foulds distance)
</li>

<li>
XML interface for PAL objects  (this uses the org.w3c.dom library which
is included with PAL - please see the
<a href="COPYRIGHT-org.w3c.dom.html">copyright info</a> of this library)
</li>


<li>...</li>

</ul>
All classes are members of one of the 16 PAL packages
(alignment, coalescent, datatype, distance, eval, gui, io, math, mep, misc,
popgen, statistics,
substmodel, tree, util, xml). A detailed list of these packages
along with a description of the public and protected
interfaces and  functions and the purpose of each single class in the library
is available in the API Documentation, included with the source archives.
<font size=-2><br><a href="#top">back to top</a></font>


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