PhyloCys

 

PhyloCys is a disulfide connectivity pattern predictor based on evolutionary information and phylogenetic trees inferred from Multiple Sequence Alignments (MSAs).

The algorithm has been designed by Gabriele Orlando, Daniele Raimondi and Wim Vranken.

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:

git clone https://eddiewrc@bitbucket.org/eddiewrc/phylocys.git

The new dataset OXCYS15 and OXCYSnr described in the paper are also available respectively from here and here.

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.

$ 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?

 

Who do I talk to?