# epytope - An Immunoinformatics Framework for Python
[](https://anaconda.org/bioconda/epytope)
[](https://anaconda.org/bioconda/epytope)
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://anaconda.org/bioconda/epytope)
[](https://anaconda.org/bioconda/epytope)
Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher
**epytope** is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. **epytope** can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods.
## Copyright
epytope is released under the three clause BSD license.
## Installation
use the following commands:
pip install git+https://github.com/KohlbacherLab/epytope
## Dependencies
### Python Packages
- pandas
- pyomo>=4.0
- svmlight
- PyMySQL
- biopython
- pyVCF
- h5py<=2.10.0
### Third-Party Software (not installed through pip)
- NetMHC predictor family (NetMHC(pan)-(I/II), NetChop, NetCTL) (<http://www.cbs.dtu.dk/services/software.php>)
- PickPocket (<http://www.cbs.dtu.dk/services/software.php>)
- Integer Linear Programming Solver (recommended CBC: <https://projects.coin-or.org/Cbc>)
Please pay attention to the different licensing of third party tools.
## Framework summary
Currently **epytope** provides implementations of several prediction methods or interfaces to external prediction tools.
- Cleavage Prediction
- Proteasomal cleavage matrix-based prediction by [Dönnes et al.](https://pubmed.ncbi.nlm.nih.gov/15987883/)
- ProteaSMM by [Tenzer et al.](https://pubmed.ncbi.nlm.nih.gov/15868101/)
- [NetChop](https://pubmed.ncbi.nlm.nih.gov/15744535/) 3.1
- Epitope Assembly
- Approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/)
- Bi-objective extension of approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/)
- Assembly with spacers by [Schubert et al.](https://pubmed.ncbi.nlm.nih.gov/26813686/)
- Epitope Prediction
- [SYFPEITHI](https://link.springer.com/article/10.1007/s002510050595)
- [MHCNuggets](https://pubmed.ncbi.nlm.nih.gov/31871119/) 2.0, 2.3.2
- [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3
- [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0
- [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3
- [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1
- [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/38000035/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3
- [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1
- [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1
- Epitope Selection
- [OptiTope](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703925/)
- Stability Prediction
- [NetMHCstabpan](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976001/) 1.0
- TAPP Prediction
- TAP prediction model by [Doytchinova et al.](https://pubmed.ncbi.nlm.nih.gov/15557175/)
- [SMMTAP](https://pubmed.ncbi.nlm.nih.gov/12902473/)
## Getting Started
Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). A reference documentation is also available [online](http://epytope.readthedocs.org/en/latest/).
## How to Cite
Please cite
[Schubert, B., Walzer, M., Brachvogel, H-P., Sozolek, A., Mohr, C., and Kohlbacher, O. (2016). FRED 2 - An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113](http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw113.short?rss=1)
and the original publications of the used methods.
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"description": "# epytope - An Immunoinformatics Framework for Python\n\n\n\n\n[](https://anaconda.org/bioconda/epytope)\n[](https://anaconda.org/bioconda/epytope)\n[](https://opensource.org/licenses/BSD-3-Clause)\n[](https://anaconda.org/bioconda/epytope)\n[](https://anaconda.org/bioconda/epytope)\n\nCopyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher\n\n**epytope** is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. **epytope** can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods.\n\n## Copyright\n\nepytope is released under the three clause BSD license.\n\n## Installation\n\nuse the following commands:\n\n pip install git+https://github.com/KohlbacherLab/epytope\n\n## Dependencies\n\n### Python Packages\n\n- pandas\n- pyomo>=4.0\n- svmlight\n- PyMySQL\n- biopython\n- pyVCF\n- h5py<=2.10.0\n\n### Third-Party Software (not installed through pip)\n\n- NetMHC predictor family (NetMHC(pan)-(I/II), NetChop, NetCTL) (<http://www.cbs.dtu.dk/services/software.php>)\n- PickPocket (<http://www.cbs.dtu.dk/services/software.php>)\n- Integer Linear Programming Solver (recommended CBC: <https://projects.coin-or.org/Cbc>)\n\nPlease pay attention to the different licensing of third party tools.\n\n## Framework summary\n\nCurrently **epytope** provides implementations of several prediction methods or interfaces to external prediction tools.\n\n- Cleavage Prediction\n - Proteasomal cleavage matrix-based prediction by [D\u00f6nnes et al.](https://pubmed.ncbi.nlm.nih.gov/15987883/)\n - ProteaSMM by [Tenzer et al.](https://pubmed.ncbi.nlm.nih.gov/15868101/)\n - [NetChop](https://pubmed.ncbi.nlm.nih.gov/15744535/) 3.1\n- Epitope Assembly\n - Approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/)\n - Bi-objective extension of approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/)\n - Assembly with spacers by [Schubert et al.](https://pubmed.ncbi.nlm.nih.gov/26813686/)\n- Epitope Prediction\n - [SYFPEITHI](https://link.springer.com/article/10.1007/s002510050595)\n - [MHCNuggets](https://pubmed.ncbi.nlm.nih.gov/31871119/) 2.0, 2.3.2\n - [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3\n - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0\n - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3\n - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1\n - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/38000035/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3\n - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1\n - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1\n- Epitope Selection\n - [OptiTope](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703925/)\n- Stability Prediction\n - [NetMHCstabpan](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976001/) 1.0\n- TAPP Prediction\n - TAP prediction model by [Doytchinova et al.](https://pubmed.ncbi.nlm.nih.gov/15557175/)\n - [SMMTAP](https://pubmed.ncbi.nlm.nih.gov/12902473/)\n\n## Getting Started\n\nUsers and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). A reference documentation is also available [online](http://epytope.readthedocs.org/en/latest/).\n\n## How to Cite\n\nPlease cite\n\n[Schubert, B., Walzer, M., Brachvogel, H-P., Sozolek, A., Mohr, C., and Kohlbacher, O. (2016). FRED 2 - An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113](http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw113.short?rss=1)\n\nand the original publications of the used methods.\n",
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