From ISOGG Wiki
Note that this list is provided for information only. Inclusion on this list does not imply recommendation or endorsement by ISOGG.
- 1 Y-STR haplotype tools (modals, genetic distance, TMRCA)
- 2 Y-STR haplogroup prediction tools
- 3 Y-SNP haplogroup prediction tools
- 4 YBrowse - The ISOGG human Y-chromosome browser
- 5 Y-STR and Y-SNP databases
- 6 General Y-DNA tools
- 7 Next generation sequencing tools
- 8 Further reading
- 9 Scientific papers
- 10 See also
- 11 References
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.
- Dean McGee's Y-DNA Utility Ysearch/FTNDA Mode, also for up to Y-DNA111 markers for Genetic Distance and TMRCA tables. It can output to PHYLIP and Fluxus for building phylogenetic trees, etc.
- The Ethio Helix Y TMRCA Calculator - two different calculators with one for STRs and one for SNPs
- TiP - the Family Tree DNA Time Predictor tool (only for FTDNA Y-DNA12+ customers)
- The Clan McDonald TMRCA Probability Calculator Graph or List
- Moses Walker's Most Recent Common Ancestor Probability Calculator Probability of Relationship %, Generations to MRCA
- Phylofriend Open source program that calculates genetic distances from Family Tree DNA projects to create phylogenetic trees with PHYLIP.
- Y-DNA Family Grouping App A free app created by Chase Ashley that allows people to quickly and easily (1) analyze surname project STR results to determine appropriate family groupings and (2) compare a particular project kit against all other kits in the project
- SAPP (Still Another Phylogeny Program). Web based interface. Takes a plain text data file (*.txt) as input. which contains the STR results, SNPs, and Genealogies for SAPP to use in building the phylogenetic tree. See the blog post from Maurice Gleeson L2 MHT - "difficult to place" people for a description of its use.
- Tim Janzen in 2008 has developed a program in Excel that does intraclade TMRCA estimates for large numbers of Y STR haplotypes. It may be downloaded from http://www.timjanzen.com/dna.html.
- Ken Nordtvedt has a program in Excel that does intraclade and interclade TMRCA estimates for Y STR haplotypes (Generations111T.xlsx only available from web.archive)
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.   
- Vadim Urasin's YPredictor (2010-2013, v1.5.0), used by scientific papers
- Nevgen Y-DNA haplogroup predictor. Milos Cetkovic Gentula and Aco Nevski, 2015
- Whit Athey's haplogroup predictor (2004-2012), used by scientific papers
- Jim Cullen's haplogroup predictor, v1.2 2008, used by scientific papers
- Arizona University's Haplogroup classifier, 2008, used by scientific papers
- Stephen P. Morse's Predicting haplogroups in one-step, allows to fetch STR-values from Ysearch or FTDNA (kit login), 2008
- Felix Immanuel's Y-Haplogroup Predictor, and Y-HaploGroup Population Browser, 2013
- Haplogroup specific:
- I: Terry Robb's haplogroup I1 and I2 subclade predictor (for 67 marker results only)
- R1b: Robert Casey's L21 Y67 subclade predictor, R-L21 Files Alex Williamson & Mike Walsh
Y-SNP haplogroup prediction tools
- Chris Morley's Y-SNP subclade predictor, optimized for Geno 2.0 data transferred to FTDNA, and also the Full Genomes demo data. See also ytree.morleydna.com.
- Felix Immanuel's 23andMe to Y-SNP Converter, 2014
- Steven Frank's AncestryDNA Reformat VBS script, 2016
- Y-DNA haplogroup converter A useful tool which allows you to enter your most downstream SNP name and see the haplogroup name using the current or historical versions of the ISOGG Y-SNP tree
- Y-Haplo A free tool provided by 23andMe for non-commercial use. The tool is designed for use with large datasets. The methodology is explained in a preprint by David Poznik Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men. BioRxiv, published online on 19 November 2016.
- Y-leaf - a tool for performing haplogroup predictions from next generation sequencing data (BAM or FASTQ files). For details see the paper by Ralf et al (2018) Yleaf: Software for human Y-chromosomal haplogroup inference from next-generation sequencing data.
YBrowse - The ISOGG human Y-chromosome browser
ybrowse.org maintained by Thomas Krahn.
- Call named SNP: ybrowse.org/gb2/gbrowse/chrY/?name=L21
- YBrowse files: Download SNP data (snps_hg19.gff3). Can be imported into XLSX/ODS or database formats by selecting "Tab" and semi-colon as separating values.
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
- YFull A raw data (BAM) interpretation and analysis service (online) for full Y-chromosome data
- Full Genomes Corporation Offers also a BAM file analysis service (Big Y etc.)
- clarifY DNA A Big Y analysis service providing personalised reports and diagrams showing placement on the phylogenetic tree. See the review by Debbie Kennett clarifY DNA - a new Y-SNP analysis service
- Brad Larkin's NextGenMatch tool. The tool is available on Brad's Genetic Homeland website. The tool is free to use but registration is required. For details see Brad's post on the GenealogyDNA mailing list
- Felix Immanuel's Big Y Download Utility A chrome add-on for use with Family Tree DNA's Big Y results
- Felix Immanuel's Big Y BAM analysis tool
- Integrative Genomics Viewer (IGV) A tool provided the Broad Institute which allows the user to analyse BAM files, needs registration with email
- Galaxy open source, web-based platform for data intensive NGS research, included are SAMtools, BamTools, Picard, VCF Manipulation, etc., User account suggested
- SNPdata A free tool for comparing build 37/19 and build 38 Y-chromosome data. it contains a search for dual SNP positions
- Testing and analysing Big Y - a primer by Dennis Wright
- Petrejcíková E, Carnogurská J, Hronská D et al (2014).Y-SNP analysis versus Y-haplogroup predictor in the Slovak population Anthropol Anz 2014;71(3):275-85.
- Schlecht J, Kaplan ME, Barnard K, Karafet T, Hammer MF, Merchant NC (2008). Machine-learning approaches for classifying haplogroup from Y chromosome STR data. PLOS Computational Biology. Published online 13 June 2008.
- Phylogeny programs
- Generation length
- Most recent common ancestor
- Mutation rates
- SNP testing
- Y-DNA SNP testing chart
- Y-DNA STR testing chart
- Autosomal DNA tools
- Raw DNA data tools
- mtDNA tools
- DNA databases
- 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
- 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
- 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