1. Installation/Program Structure
  2. ConDens Predictor
  3. ConDens Browser
  4. Structure of Alignment Input
  5. Structure of Data Output
  6. Regular Expressions in ConDens
  7. Modifying Default Program Settings
Program Structure

There is a total of two softwares: ConDens Predictor (ConDens.jar) and ConDens Browser (ConDensBrowser.jar). They should be located inside a folder named "ConDens" with sub-folders data and lib:

lib: Contains all the accessory codes of the two programs and should not be tinker with.

data: Contains information that the program can use during its runtime, which includes XML files that dictate various default settings, preset proteomes (located in data/proteins), and preset sequence alignment sets (located in data/msa).


There are 3 types of downloadable packages for the programs. The first is the complete package (recommended for first-time users) that includes both the softwares and a set of pre-available proteins and sequence alignments. Once the package is decompressed to a directory, it is ready to be used.

The second is a software-only package that excludes pre-available proteins and sequence alignments. As with the previous package, it is ready to be used once unpacked. This is the ideal package to download if the purpose of the download is to update the programs.

The third is a package that contains only the pre-available proteins and sequence alignments. In order for the contents of the package to be used, the contents of the "ConDens" folder in the package must be placed inside the parent directory of where the softwares are located.