phyloutils

A Java library for phylogenetic tree computations

• Provides functionality regarding weighted phylogenetic trees, extending the trees package.
• Parses New Hampshire (aka Newick) tree files.
• 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, and based on the FastTree 16S tree of GreenGenes sequences.

Documentation

• API docs

Download

Maven is by far the easiest way to make use of phyloutils. Just add these to your pom.xml:

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

<dependencies>
	<dependency>
		<groupId>edu.berkeley.compbio</groupId>
		<artifactId>phyloutils</artifactId>
		<version>0.921</version>
	</dependency>
</dependencies>

If you really want just the jar, you can get the latest release from the Maven repo; or get the latest stable build from the build server.