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Research through Genetics


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Welcome DNA Project DNA Project Goals Intro to DNA Testing Participation ft2dna program ft2phy program Y-DNA Results Results at FTDNA Dean McGee's Output HAM DNA Phylograms HAM Group01 Y-Search HAM Group02 Y-Search HAM Group04 Y-Search HAM Group07 Y-Search Participating Families DNA Links DNA Tools

TOOLS:

     Whit's Y-Haplogroup Predictor   by Whit Athey

     Y-DNA Comparison Utility by Dean McGee 

     Y-DNA Comparision Utility, FTDNA Mode   Dean McGee's Y-DNA Utility option for FTDNA mode

     Y-DNA Comparision Utility, 111 FTDNA Mode   Dean McGee's Y-DNA Utility option for FTDNA mode, 111 markers

     Old Comparison Utility  Excel Macros  from Dean McGee

     Terrachart  from Dean McGee.   Add haplotype group pie charts to geographic maps of the earth.

     Tools   listed at the World Families Network page

     Tools     listed at the Genetealogy web site

     Phylogeny programs   on the internet from the folks that produced the PHYLIP program

    DYS Marker Details from the Sorenson Molecular Foundation - gives the repeat  (ATCG) structure for each
marker.   This is often the input format for genetic software programs.

 
    SRM 2395 (PDF - can be used for ATCG conversion) from the National Institute of Standards and Technology

    SRM 2395   Updates since original publication.

    Tom Glad's mtDNA Analysis Utility


 STATISTICS:

    FTDNAtip  for TMRCA -  From the BLAIR DNA Project. Probabilities for a common ancestor "Y" generations ago based upon the number of matching "X" markers.

   Bill Jackson's  MRCA Probability calculator for a given number of markers and generations.

   Most Recent Common Ancestor Calculator    from Moses Walker

   TMRCA Calculator    from the Clan McDonald DNA Project

   Time to Most Recent Common Ancestor Calculator   from the Pearsall DNA Project

   Ann Turner's Mutation calculator 

   My instructions for calculating expected mutations for a Group, given the number of markers tested and years to TMRCA.

    The R package for statistical computing and graphical display.  (Not for the faint of heart. Used for more intricate research.)

    SMA (Statistics for Microarray Analysis) R package add-on for statistical analysis of genomic data. From the Speed genomic research group at Berkeley.

   Statistical software  tools from the Department of Genetics at the University of Pittsburgh



GRAPHING:

     PHYLIP   software to generate phylogenetic tree data.

          -  My Instructions for applying PHYLIP to DNA data, to create phylogenetic charts for TMRCA.

          -  Original  Instructions   for using applying PHYLIP to DNA data, by L. David Roper from the ROPER DNA Project

      MEGA   software for generating Phylogenetic and Network Tree graphs from the PHYLIP data.
  
      B.G. Galbraith's  MRCA Chart calculator  for determining probabilities, given:  markers tested, markers matched, and mutation rate.

     Phylogeny programs   on the internet. This page assembled by the folks that produced the PHYLIP program

     Fluxus Network Analysis software  from Fluxus-Engineering.  Generates evolutionary trees and networks from genetic and non-genetic data, and can then provide age estimates for any ancestor in the tree.

     Fluxus trouble shooting and FAQ's page.

SOFTWARE:

   MATHWORKS  Bioinformatics toolbox

   Phylogeny programs   on the internet assembled by the folks that produced the PHYLIP program

   LAMARC   Likelihood Analysis with Metropolis Algorithm using Random Coalescence using a Metropolis-Hastings Monte Carlo Markov Chain (MCMC) algorithm.

   Peter Beerli's web site with some software selections from the University of Washington
 

DNA MARKER STRUCTURE:

    FT2DNA     Convert individual FTDNA DYS values into ATGC format for use in various genetics programs.

    FT2PHY     Converts Dean McGee's Utility style input file into ATGC format for use in various genetics programs.


    FTDNA's  Y (or X)  Chromosome browser  - You can use this to find general marker sizes and locations.

    DYS Marker Details from the Sorenson Molecular Foundation - gives the repeat  (ATCG) structure for each
marker.   This is often the input format for genetic software programs.

     NIST  YSTR Facts   from the National Institute of Science and Technology

     Schoske's  PDF file on marker details

  Family Tree DNA's chromosome Y map of the locations for STR, SNP, and palindromes. These locations can be used for LAMARC, as well as other applications.

  
BLASTING mtDNA Full Genome Sequence (FGS) Results - Instructions from ISOGG to compare your mtDNA sequence to those from published scientific studies and other full genome sequences uploaded by commercial DNA companies.


Analysis:

    Calculating Time to Most Recent Common Ancestor (TMRCA)  by Dr. Bruce Walsh, University of Arizona, FTDNA's Advisory Board

    Time to Most Recent Common Ancestor    (PDF file) by Dr. Bruce Walsh, University of Arizona.  2001. Published by the Genetics Society of America.  The math behind the theory, for the more curious.

    Haplogroups of the World - Doug McDonald's Map (PDF file) of the distribution of Y-DNA and mtDNA

    YHRD:   Y-Chromosome Haplotype Reference Database 

    List of Products of Haplotype Group tests that can be ordered from EthnoAncestry
   
    Haplotype Group list   from EthnoAncestry

    Understanding Genetic Distance from Family Tree DNA

   YSearch - Search for your DNA ancestors by matching your markers from others around the world.
 

 On the more technical side:

   Advanced Topics in Biological Statistics  Class Lecture from 2003 by Bruce Walsh at the University of Arizona.

   A Short Tandem Repeat-Based Phylogeny for the Human Y Chromosome  - Article #182 from the American Journal of Human Genetics, volume 67.  July, 2000

   Publications from the Sorenson Molecular Genealogy Foundation

   Y Chromosome Marker Family Comparisons by L. David Roper

 Direct Determination of mutation characteristics of Y chromosome STR Loci  PDF file from the Sorenson Molecular Genealogy Foundation

   ... Locus Specific Mutation Rates for 36 Y Chromosome STRs   PDF file from the Sorenson Molecular Genealogy Foundation

    Separate marker mutation rates  from correspondence between Doug McDonald and Dean McGee in 2004 at World Families Network.

    Effective Mutation Rate at Y Chromosome STR's article posted to the American Journal of Human Genetics in January, 2004

   Likelihood-Based Estimation of Microsatellite Mutation Rates  from Genetics.org, volume 164.  June 2003

INSTRUCTIONS:
  
    PHYLIP   documentation on the web

    Guide to using PHYLIP  (PDF file) from Jarno Tuimala of the Center for Scientific Computing, Espoo, Finland.

     My Instructions for applying PHYLIP to FTDNA data, to create phylogenetic charts for TMRCA.

    Original  Instructions   for using applying PHYLIP to DNA data, by L. David Roper from the ROPER DNA Project

   Y-DNA Computational Models - my review of convenient computational models used to determine TMRCA from the Y-DNA data.

     My CONTRAST instructions for running the "contrast" program which is part of the PHYLIP program.
           Includes output from the PHYLIP "kitsch" program that has been created from
           Dean McGee's Y-DNA Comparison Utility.


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