A Java library for phylogenetic tree computations.
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README.md

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

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.