Getting Started with Phineus

To start using Phineus you must log in using the 'root' password you specified in the installation of PostgreSQL (see here)

Logging in.

After opening Phineus Select 'File' and then 'Login'

Enter your username ('root' ) and password in the dialog box and click 'Login!' as follows

After logging in the menus will be populated and you can start working.
If this is your first time running Phineus, you will need to check that Phred has been configured for Phinues successfully.

Checking Phred Installation

Select 'Tools' and then 'Install Phred':

Phineus will now check your installation of Phred and import the environmental variable you set-up when installing Phred. Once complete , you can proceed to processing tracefiles, selecting either the single plate view (for samples where all of the reads are on the same plate) or the 'High Throughput' view, which can take multiple plates of data.

Previous users of Phineus have a number of options at this point -

if you have processed data before, or if you have quit Phineus while editing sequence, you can resume that session by selecting the appropriate option.

If you have previously completed processing data and finished the session, then you can review the data from the 'Review A Complete Session' option, or you can analyse the data from the options on the Analysis menu.

Here, you can view all the data you have previously finished editing by selecting 'View and edit old data'. The resulting interface provides you with several capabilities including the capability to do comparative eburst analysis on subsets of your data, or your whole data compared to the data stored on MLST.net.

Selecting 'Help' gives you the options to review the Licence agreement for Phineus, and also to view other helpful information.

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