NodeFinder

Tools for node related operations in phylogenetic analyses

GUI Version

If you are not familiar with console or you prefer Graphical User Interface, please refer to NodeFinderGUI.

It's an GUI implementation of NodeFinder with Python tkinter.

cali.py

Do multiple calibrations at the most recent common ancestor node.

Requirements

For Linux, Windows, and Mac OS X users:

You need Python 2.6 or Python 3.x to run this script.

python cali.py

Otherwise, For Windows users:

1. If you do not have Python environment in your computer;
2. Or if you only have Python version lower than Python 2.6;

please go to this web page and download the latest version of Single-File Stand-alone Python 2.7 for Windows:

Go to Webpage: http://www.orbitals.com/programs/pyexe.html

Directly download py.exe: http://www.orbitals.com/programs/py.exe

Then run this at command line:

py.exe cali.py

Usage

Put these three files:

1. cali.py (The main script);
2. cali.ini (Config file for cali.py);
3. tree_file.nwk (The Newick tree you want to do calibration).

in the same folder, then run this command in command line:

python cali.py

Config File Syntax (cali.ini):

// Lines start with # or // will be ignored.
[Tree File Name]

    tree_file_name.nwk

[Calibration or Label Infos, One or Multiple]

    name_a, name_b, calibration_infomation_1
    name_c, name_d, calibration_infomation_2
    name_a, name_b, clade_label_information
    name, branch_label_information
    ..., ..., ...

Example One (Do calibrations):

[Tree File Name]

    test.nwk

[Calibration or Label Infos, One or Multiple]

    a, b, >0.05<0.07
    c, d, >0.08<0.09

Example Two (Add branch labels or clade labels):

[Tree File Name]

    test.nwk

[Calibration or Label Infos, One or Multiple]

    d, e, $1
    a, #1

Tips:

0. You want to run this program in Windows cmd or Command Line to see outcomes and error messages;
1. Tree file should be Newick format file (Multi lines are accepted);
2. If first line is like this: 72 1, it's OK;
3. Lines start with "#", "\" will be ignored (Considered as comments);
4. Separate elements in each line with ,;
5. Each calibration or branch label or clade label one line;
6. If calibration or branch label or clade label at specific node already exists, it will be replaced by new one;
7. A new tree file will be generated. Please check your working dir.

For Example:

Say we have a tree file: "test.nwk":

((a ,((b, c), (d, e))), (f, g));

Run this command at command line:

python cali.py

If no cali.ini file in current dir, after running the command, the program will generate this config file and gives you informations like this:

=====================================================
[Config FILE Generated]:
    Please modify [cali.ini] and run this program again.

    A test tree file was also generated: [test.nwk]
    You can do practices with: [test.nwk] and [cali.ini]
        Run this at command line --> python cali.py
=====================================================

Usage:

[cali.ini Syntax]:
    ...

[Example]:
    ...

[Tips]:
    ...

Modify cali.ini:

// Comments will be ignored
// Newick tree file name

[Tree File Name]

    test.nwk

// (Info can be: >0.05<0.07, @0.144, >0.6, #1, $1, "#1", ...)
// name_a, name_b, info
// Add '>0.05<0.07' to the most recent common node of c and b

[Calibration or Label Infos, One or Multiple]

// This is just for test, so we add calibrations and branch labels
   and clade labels at the same time.


     c, b, >0.05<0.07
     a, e, >0.04<0.06
     c, f, >0.3<0.5
     d, e, $1
     a, #1

// End

Run this command again at command line to do calibrations:

python cali.py

Then we will get a new tree with calibration informations:

((((a #1 , b), c)>0.05<0.07, (d, e)$1)>0.1<0.2, (f, g))>0.3<0.5;

And a file named "test.cali.nwk" will be genereated.

PLEASE USE SOFTWARES LIKE TreeView TO CHECK THE OUTCOME!!

        +---------- a #1
        |
        | >0.1<0.2
    +---|       +-- b
    |   |   +---| >0.05<0.07
    |   |   |   +-- c
    |   +---|
    |       |   +-- d
    |       +---| $1
----|>0.3<0.5   +-- e
    |
    |           +-- f
    +-----------|
                +-- g

INFORMATIONs and WARNINGs after Running:

1. Tipical Outcome Information:

    [2]:  a, e, >0.1<0.2
    ----------------------------------------------------
    [Name A]:   a
    [Name B]:   e
    [ Cali ]:   >0.1<0.2
    [Insert]:   c)>0.05<0.07,(d,e))),(f,g));
    [Insert]:                    ->||<-
    [Insert]:                  Insert Here
    ----------------------------------------------------
   
    # Comments:
   
    [2]: a, e, >0.1<0.2:
        This tells us the program is dealing with second calibration line now.
   
    [Insert]:
        This tells us which place to insert calibration in the Newick tree.
   

2. If calibration already exists at the node you want to add calibration, a WARNING will be given by the program:

    [Calibration Exists]:           >0.1<0.2   [- Old]
    [Calibration Replaced By]:      >0.15<0.2  [+ New]
   

3. If two lines in your cali.ini file try to add calibration at the same node, a WARNING will be given by the program:

    !!! [Warning]   Duplicate calibration:
    [Exists]:   a, b, >0.1<0.2
    [ Now  ]:   a, c, >0.2<0.3
   

   And the last line of calibration will be the final calibration at this node.