This is a stand alone version of the tree viewer in Enterobase (http://enterobase.warwick.ac.uk) It consists of an HTML and JavaScrript front end for viewing and manipulating trees and a backend written in Python and C for calculations.
EnteroMSTree - GrapeTree requires on Python 2.7 and some additional python modules (listed in requirements.txt), easiest way to install these modules is with pip:
pip install -r requirements.txt
chmod +x binaries/
On Linx or MacOSX you need to make sure the binaries in binaries/ can be executed.
If you just one to view and manupulate trees, without processing profile/fasta files, it can simply be run by opening MSTree_holder.html in a browser.
Running main.py will launch the application. This will run the lightweight webserver
python main.py
The application should open your browser to the correct page, but you can navigate there yourself (usually http://localhost:8000/).
To view a tree (newick or Nexus), just drag and drop the file into the browser window.
Runtime behaviour can be configured in grapetree/config.py
Binaries will be made available for Windows and MacOSX (see Releases).
To run tests, run pytests in the top level directory.
pytest
profile: input file. Can be either profile or fasta. Headings start with an '#' will be ignored.
method: MST or NJ
matrix_type: asymmetric or symmetric
edge_weight: harmonic or eBurst
neighbor_branch_reconnection: T or F
A string of a NEWICK tree
To run a Balanced Spanning Arborescence (BSA), use :
backend(profile=<filename>, method='MST', matrix_type='asymmetric', edge_weight='harmonic', neighbor_branch_reconnection='T')
OR simply
backend(profile=<filename>)
To run a standard minimum spanning tree :
backend(profile=<filename>, method='MST', matrix_type='symmetric', edge_weight='eBurst', neighbor_branch_reconnection='F')
To run a NJ tree (using FastME 2.0) :
backend(profile=<filename>, method='NJ')
BSA: MSTrees.py profile=<filename> method=MST matrix_type=asymmetric edge_weight=harmonic neighbor_branch_reconnection=T
MST: MSTrees.py profile=<filename> method=MST matrix_type=symmetric edge_weight=eBurst neighbor_branch_reconnection=F
NJ: MSTrees.py profile=<filename> method=NJ
Copyright Warwick University This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
EnteroMSTree - GrapeTree has not been formally published yet. If you use GrapeTree please cite the website directly: https://github.com/martinSergeant/EnteroMSTree.
An extended citation could be: Z Zhou, MJ Sergeant, NF Alikhan, M Achtman (2017) "GrapeTree: Phylogenetic visualisation for large genomic datasets", Available: https://github.com/martinSergeant/EnteroMSTree