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TroGen classifies HIV-1 V3 loop genetic sequences as either CCR5-tropic or CXCR4-using. It incorporates the TroGen algorithm, which classifies viral sequences as CCR5-tropic or CXCR4-using, based on transitions between 35 residues in close structural proximity in the V3 loop of the envelope gene of HIV-1. In addition, TroGen implements the charge rule, PSSM and SVM algorithms; the methods that are most commonly applied to tropism prediction. These machine learning algorithms can be trained using user-supplied data, or alternatively the default training model can be utilised. To classify sequences, FASTA formatted nucleotide or amino acid sequence data is loaded, and each sequence is then classified as either CCR5-tropic or CXCR4-using, at a user-specified false-positive rate.

 

This software makes use of the NetBeans Rich Client Platform (RCP) which is dual-licensed under CDDL and GPLv2.

 

In addition it makes use of the libsvm library which is distributed under the following license:

Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither name of copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

























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TroGen

Genotypic tropism prediction software for HIV

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GNU GENERAL PUBLIC LICENSE GPL v2 and CDDL V 1 1.00

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