Download biojava-alignment-5.0.0.jar file

Introduction

You can download biojava-alignment-5.0.0.jar in this page.

License

GNU LGPL v2

Type List

biojava-alignment-5.0.0.jar file has the following types. 

META-INF/MANIFEST.MF
PF00104_small.fasta
log4j2.xml
org.biojava.nbio.alignment.Alignments.class
org.biojava.nbio.alignment.FractionalIdentityInProfileScorer.class
org.biojava.nbio.alignment.FractionalIdentityScorer.class
org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer.class
org.biojava.nbio.alignment.FractionalSimilarityScorer.class
org.biojava.nbio.alignment.GuideTree.class
org.biojava.nbio.alignment.NeedlemanWunsch.class
org.biojava.nbio.alignment.SimpleGapPenalty.class
org.biojava.nbio.alignment.SimpleProfileProfileAligner.class
org.biojava.nbio.alignment.SmithWaterman.class
org.biojava.nbio.alignment.StandardRescoreRefiner.class
org.biojava.nbio.alignment.SubstitutionMatrixScorer.class
org.biojava.nbio.alignment.io.StockholmConsensusAnnotation.class
org.biojava.nbio.alignment.io.StockholmFileAnnotation.class
org.biojava.nbio.alignment.io.StockholmFileParser.class
org.biojava.nbio.alignment.io.StockholmResidueAnnotation.class
org.biojava.nbio.alignment.io.StockholmSequenceAnnotation.class
org.biojava.nbio.alignment.io.StockholmStructure.class
org.biojava.nbio.alignment.routines.AlignerHelper.class
org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner.class
org.biojava.nbio.alignment.routines.GuanUberbacher.class
org.biojava.nbio.alignment.template.AbstractMatrixAligner.class
org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner.class
org.biojava.nbio.alignment.template.AbstractProfileProfileAligner.class
org.biojava.nbio.alignment.template.AbstractScorer.class
org.biojava.nbio.alignment.template.Aligner.class
org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner.class
org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer.class
org.biojava.nbio.alignment.template.CallableProfileProfileAligner.class
org.biojava.nbio.alignment.template.GapPenalty.class
org.biojava.nbio.alignment.template.GuideTreeNode.class
org.biojava.nbio.alignment.template.HierarchicalClusterer.class
org.biojava.nbio.alignment.template.MatrixAligner.class
org.biojava.nbio.alignment.template.PairInProfileScorer.class
org.biojava.nbio.alignment.template.PairwiseSequenceAligner.class
org.biojava.nbio.alignment.template.PairwiseSequenceScorer.class
org.biojava.nbio.alignment.template.PartitionRefiner.class
org.biojava.nbio.alignment.template.ProfileProfileAligner.class
org.biojava.nbio.alignment.template.ProfileProfileScorer.class
org.biojava.nbio.alignment.template.RescoreRefiner.class
org.biojava.nbio.alignment.template.Scorer.class
org.biojava.nbio.phylo.Comparison.class
org.biojava.nbio.phylo.DistanceMatrixCalculator.class
org.biojava.nbio.phylo.DistanceTreeEvaluator.class
org.biojava.nbio.phylo.ForesterWrapper.class
org.biojava.nbio.phylo.TreeConstructor.class
org.biojava.nbio.phylo.TreeConstructorType.class
org.biojava.nbio.phylo.TreeType.class

Pom

biojava-alignment-5.0.0.pom file content. 

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>5.0.0</version>
	</parent>
	<artifactId>biojava-alignment</artifactId>
	<name>biojava-alignment</name>

	<licenses>
		<license>
			<name>GNU LGPL v2</name>
			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<url>http://www.biojava.org</url>
	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
	</properties>
	<build>
		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes 
				(demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>
		
		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>5.0.0</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava.thirdparty</groupId>
			<artifactId>forester</artifactId>
		</dependency>
		<!-- logging dependencies (managed by parent pom, don't set versions or 
			scopes here) -->
		<dependency>
        	<groupId>org.slf4j</groupId>
        	<artifactId>slf4j-api</artifactId>
    	</dependency>
    	<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-slf4j-impl</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-api</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-core</artifactId>
  		</dependency>
	</dependencies>
</project>

POM Entry 

<dependency>
   <groupId>org.biojava</groupId>
   <artifactId>biojava-alignment</artifactId>
   <version>5.0.0</version>
</dependency>

Download

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Download biojava-alignment-5.0.0.jar file




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