From ISOGG Wiki
Note that this list is provided for information only. Inclusion on this list does not imply recommendation or endorsement by ISOGG.
List of mtDNA tools
- James Lick's mtHap utility A tool for checking and assigning mtDNA haplogroups on an individual basis. It provides a detailed assignment showing the SNP path and also gives a list of alternatives. The tool is usually updated within 24 hours of the release of each new Phylotree build.
- YSEQ mt Clade Finder A new tool developed by Hunter Provyn and Thomas Krahn. It will provide a haplogroup assignment from a FASTA file based on the experimental YFull mtDNA tree.
- Haplofind The tool is described in: Vianello D, Sevini F, Castellani G, Laura L, Capri M, Franceschi C. Haplofind: A new method for high-throughput mtDNA haplogroup assignment. Human Mutations 2013 May 20. [Epub ahead of print]. This tool can be used for batch-processing mtDNA haplogroup assignments and will also analyse sequences for medically informative associations. It only accepts FASTA files.
- HaploGrep 2 An automated tool for determining haplogroups. The tool will accept VCF files from whole genome sequencing data. For details see the article by Weissensteiner et al (2016) on HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing
- Ian Logan's Haplogroup Finder
- Ian Logan's GENbank mtDNA sequence checker
- Ian Logan's mtDNA mutation computer model
- mitoYDNA.org A crowdsourced Y-DNA and mtDNA database with tools and analysis.
- mtDNA Profiler The tool is described in: Yang IS, Lee HY, Yang WI, Shin KJ. mtDNAprofiler: A Web Application for the Nomenclature and Comparison of Human Mitochondrial DNA Sequences. Journal of Forensic Science. 2013 May 17. [Epub ahead of print]
- mtPhyl, a free software tool for human mitochondrial DNA analysis and phylogeny reconstruction
- PhyloGeographer mt Heat Map A tool developed by Hunter Provyn and Thomas Krahn providing relative frequency maps for mtDNA haplogroups
- Tom Glad's mtDNA analysis utility
- Ybrowse Human mitochondrial DNA on Ybrowse
- YFull The company maintains an independent mtDNA tree and offers an mtDNA analysis for a fee
No longer available/supported/maintained
- Doug McDonald's TMRCA calculator is no longer available or supported but can be found via the wayback machine by clicking here. For instructions on using the calculator for mtDNA results see the article by Charles Kerchner An example of how to use TMRCA calculators for mtDNA test results
- Martin Richards' mtDNA mutation rate calculator (broken link)
- Felix Immanuel's Genetic Genealogy Tools are no longer available or supported but can be found via the wayback machine by clicking here.