Download OrthoSelect User Guide

6
Long Version - Preliminary Work
Contrary to the previous section, this section gives a more theoretical and detailed overview of all available options and parameters of OrthoSelect. Taxa
names in this section are used as examples only. They should be replaced by
the real taxa names in the study.
6.1
Preliminary steps
The section describes some preliminary steps to prepare your system and the
data for the analysis. It covers the download and installation of external programs as well as the selection of an ortholog database and a final check if everything is correctly set up.
6.2
Required external Programs
The following external programs need to be installed on your system. Download
and install them. Make sure that all programs are accessible from the command
line1 . The tested versions of the program are in brackets.
• BioPerl (Version 1.5.1)
• BLAST (Version 2.2.18)
• ESTScan (Version 2-2.1)
• Wise (Version 2.2.0)
• HMMER (Version 3 alpha)
• Clustalw (Version 2.0.8)
• T-Coffee (Version 5.72) or Muscle (Version 3.7)
• Gblocks (Version 0.91b)
• Noisy (Version 1.5.7)2
6.3
Automatical download of required programs
Alternatively, you can use a script that automatically and installs all required
programs. The script has been tested with Macosx 10.5.2, Ubuntu (32-bit), and
the bash shell (which is the default shell).
1 You can check this manually by entering the program name in the command line. If the
program starts, it is installed and accessible, if not, then an error message with inform you
2 Due to difficulties installing this software we do not offer to automatically install these
software. Nevertheless, Noisy - manually installed - can be used by OrthoSelect.
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