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Welcome to the CompOmics environment wiki. These wiki pages contain general information about the different tools hosted by the CompOmics group. Some tools have their own repository and wiki, more information can be found on the general Github page.

• IdentificationParametersCLI This command line application allows you to generate identification parameters in the json format supported among our tools.

• JavaTroubleShooting This page provides help with common Java related issues that one can encounter when using software from the CompOmics group.

• PeptideMapper PeptideMapper is a lightweight and efficient application for the mapping of amino acid sequences and sequence tags onto protein databases in the fasta format.

• PeptideMapperCLI This command line application allows you to use our PeptideMapper on lists of peptide sequences or sequence tags.

• ProteinInference This page provides background and help on protein inference problems.

• Usage As Dependency Most of our back-end code is stored in the compomics-utilities package and can be used as dependency in other application. The code is written in java under the permissive Apache 2.0 license.