realmizat/nodefindergui

GUI for NodeFinder Program

NodeFinderGUI

GUI for NodeFinder Program

Introduction

This is GUI implementation for NodeFinder program, used for adding information to bipartition/multifurcating Newick format phylogenetic tree:

1. Calibration info;
2. Clade Label;
3. Branch Label

Download

Please download the latest zipped file: NodeFinderGUI.zip

If you don't need the README file and the Demo GIF file, just download the NodeFinder.pyw file or nodefinder_gui.py file.

If the pyw file does not work, please try the nodefinder_gui.py file. The compiled byte code .pyw file is essentially a .pyc file that was compiled by the Python interpreter to byte code, then changed extension to .pyw. It's faster to launch on slow computers since no more source code -> byte code procedure need to be done.

Usage

NodeFinderGUI supports Python >= 2.7 or Python >= 3.3.

Unzip NodeFinderGUI.zip, then,

• Double click the latest compiled byte code pyw file NodeFinderGUI.pyw
• Or double click nodefinder_gui.py
• Or use import noderfinder_gui.py.

Command Line Version

• NodeFinderC (recommended), C implementation of NodeFinder.
• nodefinder-go (recommended), Go implementation of NodeFinder.
• NodeFinder, Python command line version.

Simple Usage

Config line syntax:

name_a, name_b, calibration_infomation
name_a, name_b, clade_label_information
name, branch_label_information
..., ..., ...

Input tree need to be Newick format phylogenetic tree. For example:

(human, (cat, dog));

You can add multiple lines at the same time. The program will finish all operations automatically.

Please refer to NodeFinder for more detailed usage and other information.

Demo

Input:

AF083022_Poikilolaimus_regenfussi, AF083017_Rhabditoides_inermiformis, >0.109<0.317
AF083022_Poikilolaimus_regenfussi, DQ094172_Ascarophis_arctica, >0.222<0.358

Output log:

[1]:  AF083022_Poikilolaimus_regenfussi, AF083017_Rhabditoides_inermiformis, >0.109<0.317
----------------------------------------------------
[Name A]:   AF083022_Poikilolaimus_regenfussi
[Name B]:   AF083017_Rhabditoides_inermiformis
[ Info ]:   >0.109<0.317
[Insert]:   toides_inermiformis),((((((((DQ094172_As
[Insert]:                       ->||<-                  
[Insert]:                    Insert Here               
----------------------------------------------------


[2]:  AF083022_Poikilolaimus_regenfussi, DQ094172_Ascarophis_arctica, >0.222<0.358
----------------------------------------------------
[Name A]:   AF083022_Poikilolaimus_regenfussi
[Name B]:   DQ094172_Ascarophis_arctica
[ Info ]:   >0.222<0.358
[Insert]:   helenchus_avenae)))),AF036607_Teratoceph
[Insert]:                    ->||<-                  
[Insert]:                  Insert Here               
----------------------------------------------------

Implementation

Given two species, this program finds all ancestor nodes for each species by using stack (to exclude other monophyletic group) and parenthesis. Then compare these two ancestor node list and find the index of most recent common ancestor nodes.

For example:

List of ancestor nodes index:
species1:     [57, 62, 73, 102, 162, 214, 258]
                            ^    ^    ^    ^
                            |    |    |    |
species2: [39, 48, 81, 94, 102, 162, 214, 258]

Then 102 will be the index of most recent common ancestor node.