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Research through Genetics

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Welcome DNA Project DNA Project Goals Intro to DNA Testing Participation Post DNA to HAM Country Privacy Statement Release of Liability Y-DNA Results Results at FTDNA Dean McGee's Output HAM DNA Phylograms Participating Families HAM Group01 Y-Search HAM Group02 Y-Search HAM Group04 Y-Search HAM Group07 Y-Search ft2dna program ft2phy program 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.

     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.

    mtDNA Tools mtDNA Analysis Tools at ISOGG

 STATISTICS:

   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 (2014 version)

   TMRCA STR SNP Chart    Iain McDonald's TMRCA Chart of Years given STR GD and # of SNPs

   TMRCA STR SNP Python Program    Iain McDonald's TMRCA Python Program at GitHub using STRs and SNPs

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

   Ann Turner's Mutation calculator 

    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.
  
     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.

 
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.

    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

   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:

    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:


   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

    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.


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