YFull: FAQ↩ Back 

Q: How many subclades have been added to the MTree, and what is YFull's policy on using GenBank samples?

A: We have already expanded the MTree by adding nearly 15,000 subclades, and we continue to enrich our mtDNA database with new subclades every day. The total number of subclades in the tree is always indicated in the lower left corner of the MTree page.

However, it is important to note that we did not download all available samples from GenBank. We are committed to respecting privacy concerns and therefore only utilize data from scientific articles, excluding samples directly submitted from labs. 
Additionally, we would like to inform our users that currently, we are only analyzing FASTA files. 

References:

For constructing the MTree YFull uses data from their customers and data from GenBank The initial version of MTree was based on the PhyloTree 17 of van Oven (18 Feb 2016). See van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. PhyloTree.org. doi:10.1002/humu.20921

Also, YFull used some information from Ian Logan's website.

The formula of calculation of the phylogenetic weight of mutation based on HaploGrep principes See Weissensteiner H., Pacher D., Kloss-Brandstätter A., Forer L., Specht G., Bandelt H.-J., Kronenberg F., Salas A., Schönherr S. 2016. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucl. Acids. Res. 2016 Apr 15; doi:10.1093/nar/gkw233

For the mtDNA haplogroup classification, YFull uses Kulczynski distance. See Kloss-Brandstätter A., Pacher D., Schönherr S., Weissensteiner H., Binna R., Specht G., Kronenberg F. 2011. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups< Hum Mutat. 2011 Jan;32(1):25-32. doi: 10.1002/humu.21382. Epub 2010 Nov 16.

Last updated May 29, 2024.