A Java library for phylogenetic tree computations

  • Provides data structures for weighted phylogenetic trees.
  • Parses New Hampshire (aka Newick) tree files.
  • Provides various operations on trees (such as extracting subtrees, tree union and intersection, and such).
  • Computes phylogenetic alpha and beta diversity measures, such as Weighted UniFrac.
  • Computes phylogenetic distances between species based on the Ciccarelli et al. 2006 tree of life.

Documentation

Download

Phyloutils has dependencies on other libraries; Maven is by far the easiest way to deal with this. To use phyloutils in your Maven project, just add these to your pom.xml: 

<repositories>
	<repository>
		<id>dev.davidsoergel.com releases</id>
		<url>http://dev.davidsoergel.com/artifactory/repo</url>
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
	</repository>
	<repository>
		<id>dev.davidsoergel.com snapshots</id>
		<url>http://dev.davidsoergel.com/artifactory/repo</url>
		<releases>
			<enabled>false</enabled>
		</releases>
	</repository>
</repositories>

<dependencies>
	<dependency>
		<groupId>edu.berkeley.compbio</groupId>
		<artifactId>phyloutils</artifactId>
		<version>0.9</version>
	</dependency>
</dependencies>

If you really want just the jar, you can get it here: phyloutils-0.9.jar (56 KB) May 9, 2008

Or get the latest stable build from the continuous integration server.

You can also browse the source, or get the source with svn: 

svn co http://svn.davidsoergel.com/repos/phyloutils/trunk phyloutils

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