Page Actions

Y-DNA tools

From ISOGG Wiki

There are a number of Y-DNA tools that can be used to analyse Y-chromosome DNA results including predicton of haplogroups.

Note that this list is provided for information only. Inclusion on this list does not imply recommendation or endorsement by ISOGG.

Y-STR haplotype tools (modals, genetic distance, TMRCA)

The following is a selection of tools that can be used for a set of Y-STR values (DYS etc.) including calculating the time to the most recent common ancestor.

Y-STR haplogroup prediction tools

The accuracy of haplogroup prediction based on Y-STR haplotypes depends mainly on the number of STR-values. Without SNP confirmation prediction for low-resolution haplotpyes (Y-STR12 to Y-STR24) has a low value of confidence and convergence can be a problem. For many haplogroups Y-STR25 to Y-STR37 has an acceptable confidence level while for some young haplogroups with rapid diversification and expansion like in R1b even Y-STR67 is not enough to discriminate the correct sublineage with confidence. A few scientific studies are available. [1] [2] [3]

Y-SNP haplogroup prediction tools

YBrowse - The ISOGG human Y-chromosome browser

ybrowse.org maintained by Thomas Krahn.

Y-STR and Y-SNP databases

  • MitoYDNA A crowdsourced Y-DNA and mtDNA database
  • YHRD.org, World Y-database with over 160,000 haplotypes, 1015 populations, 33 metapopulations, Sascha Willuweit & Lutz Roewer, 2000-2016
  • Semargl.me A website for haplotype searches (FTDNA, SMGF, etc.), TMRCA calculations, etc
  • Ysearch public haplotype database and searches (mainly FTDNA)
  • Yfiler haplotype database

General Y-DNA tools

  • Ancestral DNA Market Pedigree Display A tool from Brad Larkin which allows the user to display the SNP progression for a single ancestral line
  • Genetic Homeland DNA Marker Index A free resource from Brad Larkin which provides an index of markers and their RSID positions on all 23 chromosomes.
  • FT2DNA Dave Hamm's utility to convert Family Tree DNA's Y-chromosome repeat data format into raw code (i.e.: ATGC) for analysis by other utilities such as PHYLIP.
  • FT2PHY Dave Hamm's tool for the conversion of FTDNA repeat data format files into ATGC format files for use with PHYLIP compatible packages, such as DNAML. This program uses input that is compatible with Dean McGee's Y-DNA Utility, but is limited to 37 markers.
  • Ann Turner's downloadable program for computing mutation rates
  • YGED Roger Arrick's program simplifies the creation of GEDCOM files for the Y-DNA line

Next generation sequencing tools

Further reading

Scientific papers

See also

References

  1. Wang et al 2013 (preprint): Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction, http://arxiv.org/abs/1310.5413
  2. Larmuseau et al 2014: Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance, http://dx.doi.org/10.1111/ahg.12050
  3. Woźniak et al 2006: Correlations between haplogroup membership and Y-STR haplotype as a potential measure of quality control in forensic examinations [in Polish], http://www.ncbi.nlm.nih.gov/pubmed/17131759