FT2PHY

by Dave Hamm, Franklin, Ohio  - copyright 2009

                                        

 Conversion of Family Tree DNA "repeat" data format into "ATGC" format.


 Designed to convert FTDNA data to ATGC format for use in other genetic software utilities.

QUICK START:


From a Windows command line window (Start/run/cmd):


   <ft2phy> <name of input file>


As in:


   ft2phy     HAM_to_paste_into_McGee.txt


Where the text file "HAM_to_paste_into_McGee.txt" would be data used to cut-and-paste into Dean McGee's Utility.

This program differs from the "ft2dna" program in that it will accept a full line of repeat values from a file that is compatible with Dean McGee's Y-DNA Utility.

The ft2phy program does NOT have a GUI interface, so you need to run it from a command line window.


Download FT2PHY   version 1.0 package   (compiled with GCC for Windows XP)

OVERVIEW:


  Overview for the use with PHYLIP "DNAPARS," "CONSENSE," PHYML, Tree Puzzle, LAMARC, etc.


FT2PHY is a set of program to convert individual DYS repeat values given by FTDNA into "ATGC" format for use with genetics programs, or any other program requiring the ATGC structure in what is known as the "PHYLIP" format.


FT2PHY was primarily  written for use with LAMARC, but with some editing, the output can be used with any number of genetics programs that require the "PHYLIP" format.


That basic format is usually of the form:


a) The first line usually consists of the number of taxa and the size (number of characters) of each line of the data.
b) The lines containing data have the first ten characters reserved for the  name identifier.
c) The data has been converted into ATGC format.

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The PHYLIP package contains software to generate phylogenetic tree data.

The PHYLIP web site is located at:

   http://evolution.genetics.washington.edu/phylip.html


Lamarc does some Bayesian or Likelihood analysis with multiple genomic regions, recombination rates, and migration rates.

The LAMARC web site:

 
     http://evolution.gs.washington.edu/lamarc/index.html


MEGA software is used for generating Phylogenetic and Network Tree (diagrams) from the PHYLIP data.


    http://www.megasoftware.net/

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To Create an icon for the Windows Desktop:
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Find the MS-DOS prompt:
From your desktop find the "Start Button" on the lower left corner.
Click on:        Start > Programs > Accessories
The MS-DOS Prompt is in the Accessories Menu.
Right Click the MS-DOS Prompt Icon and drag it to your desktop and create a shortcut on your Desktop.

- Right click on the newly created Desktop icon and select "Rename."  Rename it to FT2PHY.
- Right click on the newly created Desktop icon again and select "Properties."
   Under the "Shortcut" tab, there is a box for "Start in:"  _____
   Type the full path to the FT2PHY executable in this "Start in:" box.

     example:     K:\Data\Genealogy\DNA\FT2PHY1.0

- Click on "Apply."

If you wish to change the command line options for font color or background colors, select the "Colors" tab.
(For example, I use a gray background with a blue font.)

When you are done, click on "Apply" then "OK"

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If you have not created a Desktop icon:
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To start a "command line window" from Microsoft Windows:

 - click on "START"

 - click on "RUN"

 - type in "cmd" (without the quotes)

 - click on "OK"


 a command line window should appear.

Then, you need to "cd" to change directory to where the conversion routines are located.


  cd /D E:\Data\DNA


  when done, you can return to your default directory with:


  cd /D C:

To create the converted values for DYS439, then, run the program from a command line

interface, and provide the number of repeats as an argument:


   ft2phy <name of your data file>


As in:


   ft2phy     HAM_to_paste_into_McGee.txt 


As a reminder, for PHYLIP compatible programs, you will need to copy all 37 DYS marker data files into one file.

 - Dave Hamm   


Franklin, Ohio

HAM Surname DNA Project Coordinator

email: odoniv@earthlink.net

URL: http://home.earthlink.net/~odoniv/HamCountry/HAMCountry.html


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