How to use Mallard
1. Starting the program
Mallard can be started in one of two ways, depending on the computer's
operating system.
- Microsoft Windows and Apple Mac
OS X users: Go to the directory containing the Mallard.jar file
and mouse-click the Mallard.jar file icon.
- All users: From the command line, run the program with the
command java
-jar
Mallard.jar (remembering to include the full path of the jar
file if starting from a different directory to that of the jar file).
2. Entering data into the program
Mallard requires that the sequences to be checked should be in a
multiple sequence alignment which includes a full-length reference
sequence for supplying positional information (for example Escherichia
coli K12 U00096). Furher details on
correct file format can be found here.
To open an input file, go to the File menu and select Open
Sequence File.
File loaded, the contents are displayed within the dataset panel -
displays accession, thumbnail image of alignment, sequence
length. All records are initially selected for inclusion in the
analysis. This can be changed by mouse-clicking the selected icon
of inidividual records, or by highlighting the records to change and
using the buttons provided below the panel.
3. Generate DE plot.
Press Run to analyse dataset (The analysis can be aborted at any stage
by pressing abort button.) - each record will be compared with each
other generating DE values which are plotted against mean %
differences. In essence, each DE value summarises a single
pairwise comparison; the position of a DE value within the plot
indicates whether that comparison is unusual - that is involves one or
more anomalous sequences. Further information on DE values and
what they represent can be found here.
Individual DE values can be explored by mouse-clicking the data-point -
the corresponding Pintail plot is presented.
4. Identify outlier DE values
Select Identify Outliers to identify unusually high DE values
