Biology Reference
In-Depth Information
Fig. 1 Contents of the SAT ´ software package. The SAT ´ application is represented by the rightmost icon.
The “doc” folder contains software documentation. The “data” folder contains example input files, and the
corresponding output files are contained in the “sample-output” folder
1. If the input sequence file is not in FASTA format, use a third-
party program to convert the input file to FASTA format. See
Note 12 .
2. We recommend that a new output folder be created for each
SAT´ analysis.
8.2 Preparing Input
File and Output Folder
1. After starting the SAT´ program, the main analysis window
appears (Fig. 2 ). The default settings correspond to the
“SAT´-II fast” analysis described in [ 24 ], which are appropriate
for a wide range of phylogenetic studies. Make sure that the
“SAT´-II-fast” option is selected in the “Quick Set” drop-
down menu.
2. Click the “Sequence file” button to load the input file. Locate
and select the FASTA-formatted input file in the dialog box.
3. A dialog box appears with a query about automatic customiza-
tion of some analysis settings based on the input file (Fig. 3 ).
Click “OK” to enable the automatic customization. Custo-
mized settings will be reflected in the “SAT´ Settings” box of
the application.
4. In the “Decomposition” drop-down menu, select “Centroid”.
If this changes the current defaults, the “Quick Set” menu will
change to the “(Custom)” option.
5. In the “Job Name” field, provide a unique name for the analysis.
6. Click the “Output Dir.” button. Locate and select the desired
output folder in the dialog box. If output files for a job with the
same name exists in the output folder, the output files of the
current analysis will contain an additional integer to prevent file
collisions.
8.3 Basic Analysis:
Nucleotide Datasets
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