The pre-generated testfiles and saved results are used when POPE is run as follows:
You can download POPE in the same way as described above for Linux and Mac's, from the DOS terminal. Alteratively you can use Webstart to dowload POPE (Under construction - link will be added....).
In order to prevent JRE memory problems, run as follows:
POPE requires access to a number of files in order to run properly. An example of each file can be found in a folder called testFiles, whithin the Pope folder (when Pope is downloaded)
The configuration file is generated in the pope folder the first time Pope is run. It tells pope where to find certain files and which file extensions are in use. The configuration file has the following format: config
Example of the external programs file: extPrograms
When POPE is run like:
java -jar Pope.jar
An input file in the following format: input file is required by POPE in order to conduct a phylogenetic reconstruction followed by phylogenetic analysis. The input file can contain one or more sequences in Fasta format. The sequence identifier has to include the species name abbreviation (2 characters) followed by an underscore, followed by the sequence identifier itself.
Example:
Dm_CG2259 (where Dm is the abbreviation for Drosophila melanogaster and CG2259 is the Ensembl identifier of the sequence)
or
Hs_ENSP00000229416 (Homo sapiens and the Ensemble sequence identifier)
The sequences in the database have to be in the same format as the input files described above. I.e, each sequence in the database has to be represented by its species (two letter abbreviation) and the sequence identifier.
The database needs to be formatted before it can be used:
Command to format the database:
formatdb -p T -i database
In order to run POPE with the config option, POPE needs to be told where the pre-generated blast, homologue, alignment and tree files are. All the sequences included in all files have to have the identifier in the same format as described for the above (2 letter species abbreviation followed by underscore, followed by the sequence identifier).