Install Multiple sequence alignment

Installation Step 1:

Download strap.jar (3.3 MByte) to the desktop. It can be deleted later.

Installation Step 2 for Windows:
Download the Batch file strap.bat to the desktop.

To start, double click strap.bat Installation Step 2 for Linux:
Download the script file strap.sh to the desktop. Typically, the zip file will be opened in an archive manager and you can drag the file strap.sh to the desktop with the mouse.

Starting Strap:
Double click the file strap.sh or enter the command line:

          ~/Desktop/strap.sh

Installation Step 2 for MacOSX:
Download the command file strap.command to the desktop.

To start Strap double click the file strap.command.

Open the script file (from installation step 1) using a text editor:

Web-Proxy: On some machines, Strap can not access the internet. The reason is that the system wide is not automatically recognized by Java.
Solution: Go to the text line with the java command and remove any proxy-option from this line like "-probeWebProxy" or "-sysProxies". Enter your web proxy settings directly after the java-command in the following form:
```
            -Dhttp.proxyHost=realproxy.charite.de -Dhttp.proxyPort=888 
          
```
OutOfMemoryError: The parameter in the form -Xmx200M sets the maximum memory limit to 200 MByte. Increase in case of OutOfMemoryError.
The java version Consider the line with the Java command. The computer will search for the Java command on the hard disk according to the environment variable PATH. Instead of the command "java" the full file path to the "java" program can be given such as "/usr/bin/java" or "C:\Programs\java\jre6\bin\java.exe" (Windows).

Protein/alignment file conversion: Use command line options -toFasta, -toMultipleFasta, -toClustal.
Strap can be used as a text viewer for very large files with advanced search text highlighting. Use the command line option -textViewer.
Strap can be used to manage pubmed abstracts and PDF full text. Text pattern highlighting allows text mining by eye in large amounts of pubmed abstracts. Use the command line option -pubmed.

Local Installation of Strap