@happykhan happykhan released this Jul 5, 2018 · 4 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click) then open the extracted folder and run GrapeTree_mac. You may be warned about Security settings, if you right click on the GrapeTree binary and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to unzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

Change Log

  • Added RAPID-NJ as another tree inference method.
  • Fixed Help text for EnteroBase (?) goes outside of the box.
  • Fixed Group number setting doesnt show other.
  • Fixed Crashing on larger datasets on Windows 10
  • Fixed context menu going out of frame

@happykhan happykhan released this Apr 19, 2018 · 74 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click) then open the extracted folder and run GrapeTree_mac. You may be warned about Security settings, if you right click on the GrapeTree binary and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to unzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

Change Log

  • Hotfix for FastME Binary, so that it works out of the box on Linux distros.

@happykhan happykhan released this Apr 18, 2018 · 89 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click) then open the extracted folder and run GrapeTree_mac. You may be warned about Security settings, if you right click on the GrapeTree binary and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to unzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

@happykhan happykhan released this Apr 12, 2018 · 172 commits to master since this release

Assets 3

Using GrapeTree
GrapeTree is a novel visualization component within EnteroBase. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Many people have asked for a stand-alone version of GrapeTree that they could use offline or integrate into the other applications. The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be an executable you can drag into your Applications folder.

You may be warned about Security settings, if you right click on the GrapeTree app and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to untzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

@happykhan happykhan released this Nov 8, 2017 · 257 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a novel visualization component within EnteroBase. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Many people have asked for a stand-alone version of GrapeTree that they could use offline or integrate into the other applications. The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be an executable you can drag into your Applications folder.

You may be warned about Security settings, if you right click on the GrapeTree app and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to untzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

Change log

  • Updated examples with those included in manuscript.
  • Added simulation data
  • Improved performance for larger trees
  • Reduced the max number of visible nodes
  • Renamed neighbor_branch_reconnection to branch_recrafting
  • Updated sorting performance issues.
Nov 7, 2017
function for calc distance matrix
Pre-release

@happykhan happykhan released this Aug 2, 2017 · 310 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a novel visualization component within EnteroBase. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Many people have asked for a stand-alone version of GrapeTree that they could use offline or integrate into the other applications. The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be an app you can drag into your Applications folder.

You may be warned about Security settings, if you right click on the GrapeTree app and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to untzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

Change log

  • Added Menu Help buttons and help text
  • Fixes for left-hand button layout, should be more intuitive.
  • Fixes for Integration into EnteroBase
  • Removed some redundant buttons (load metadata)
  • Fixes for right click menu
  • Ability to restore original layout (nuke all changes)
Pre-release

@happykhan happykhan released this Jul 10, 2017 · 358 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a novel visualization component within EnteroBase. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Many people have asked for a stand-alone version of GrapeTree that they could use offline or integrate into the other applications. The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be an app you can drag into your Applications folder.

You may be warned about Security settings, if you right click on the GrapeTree app and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.zip

Once downloaded, you will need to untzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.

Jul 10, 2017

@happykhan happykhan released this Jul 4, 2017 · 363 commits to master since this release

Assets 4

Using GrapeTree
GrapeTree is a novel visualization component within EnteroBase. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Many people have asked for a stand-alone version of GrapeTree that they could use offline or integrate into the other applications. The stand-alone version presented here emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results.

Detailed documentation is available here: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree

Running on Mac: Download GrapeTree_mac.zip

You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be an app you can drag into your Applications folder.

You may be warned about Security settings, if you right click on the GrapeTree app and then click "Open" it should be fine.

Running on Windows: Download GrapeTree_win.exe

Once downloaded, double click GrapeTree_win.exe to start GrapeTree. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: "More info", and then the button "Run Anyway".

Source code
Source code is available in tar.gz or zip format.