rMSA_INSTALL: Installing Third-Party Software for rMSA

In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

Description

How to install third-party software for rMSA for Linux, OS X and Windows.

Linux (Ubuntu/Debian)

Use the package manager to install packages:

• clustal

• kalign

• mafft

• muscle

• boxshade (also needs package ghostscript)

OS X

• ClustalW: Install from http://www.clustal.org/.

• Kalign: Install from http://msa.sbc.su.se/cgi-bin/msa.cgi by downloading and installing the source of Kalign (current).

• MAFFT: Install from http://mafft.cbrc.jp/alignment/software/.

• MUSCLE: Install from http://www.drive5.com/muscle/.

• Boxshade is currenly not available for OS X (you can download it from http://boxshade.sourceforge.net/ and compile it with the free pascal compiler and install ghostscript).

Windows

• ClustalW: Install from http://www.clustal.org/.

• Kalign: Download kalign.exe from http://www.tcoffee.org/Packages/Binaries/windows/.

• MAFFT: Download mafft.exe from http://www.tcoffee.org/Packages/Binaries/windows/.

• MUSCLE: Install from http://www.drive5.com/muscle/.

• Boxshade is currenly not available for Windows

Setting the PATH variable for Windows

1. From the Desktop, right-click My Computer and click Properties.

2. Click Advanced System Settings link in the left column.

3. In the System Properties window click the Environment Variables button.

4. Add the folder(s) with the executables to the PATH variable (separated by ;)

5. Restart your R session.

6. Try the following in R: Sys.which("clustalw") This should show you where it found the executable

mhahsler/rMSA documentation built on May 22, 2019, 8:55 p.m.