PhyloCys is a disulfide connectivity pattern predictor based on evolutionary information and phylogenetic trees inferred from Multiple Sequence Alignments (MSAs).
The python implementation of the prediction algorithm can be downloaded, along with PDBCYS and SPX datasets described in the paper from its git repository. It is possible to install it by cloning the repository, with the command:
Requirements and Disclaimer:
The code is released under GNU GPL and privileges demonstrative purposes and portability; more efficient implementations can be easily written in languages others than python, but in this case the bottleneck is situated in the phylogenetic trees construction, that is computationally hard problem. The current implementation requires ETE2 library and ClustalW.
- ETE2 (https://pypi.python.org/pypi/ete2/) can be installed on debian-like systems with the following commands:
$ sudo apt-get install python-setuptools python-numpy python-qt4 python-scipy python-mysqldb python-lxml
$ sudo easy_install -U ete2
CLUSTALW binaries can be downloaded from here http://www.clustal.org/download/current/ and the executable file must be placed in "clustalBins" folder
We strongly recommend to use HHblits alignments as input because building phylogenetic trees for bigger alignment is unfeasible. A local instance of HHblits can be downloaded and installed on your local machine from here.
- In order to provide the best tool possible, we are very grateful for bug reports!
How do I set it up?
- First clone the repository on your local machine with the command "git clone https://firstname.lastname@example.org/eddiewrc/phylocys.git" or by downloading the latest compressed archive in the DOWNLOAD section
Who do I talk to?