BioConductor

msa 1.12.0

Multiple Sequence Alignment

Released Apr 27, 2018 by Ulrich Bodenhofer

This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and no tests could be found for the package.

Dependencies

Biostrings 2.48.0 BiocGenerics 0.26.0 IRanges 2.14.10 Rcpp S4Vectors 0.18.3

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Installation

Maven

This package can be included as a dependency from a Java or Scala project by including the following your project's pom.xml file. Read more about embedding Renjin in JVM-based projects.

<dependencies>
  <dependency>
    <groupId>org.renjin.bioconductor</groupId>
    <artifactId>msa</artifactId>
    <version>1.12.0-b4</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

View build log

Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.bioconductor:msa')

Source

C++