What is HaploFind?

Well, initially HaploFind used to be "just" a high throughput algorithm to perform complete mtDNA sequences classification according to haplogroup nomenclature. At the moment, instead, represent a complete Web Application focused on mtDNA complete sequences annotation. It's based on PhyloTree phylogenetic tree, and uses Mitomap as a source for annotation data.

So, what it's able to do?

Haplogroup classification represent only the starting point of mtDNA analysis, more information is needed to understand the complete picture. For this reason, HaploFind annotates all the variations (SNPs or INDELS) found in the sequences with data regarding syn/non syn mutations, disease associations and if each particular mutation was expected in the assigned haplogroup or not. And everything can be easily exported in various formats, starting from Excels (.xlsx), to YAML, if you need to further analyze the data programmatically.

Sounds complicated. Which strange format should I have to use this tool?

Nothing complicated. Really. Just upload your complete sequences in a single FASTA format file, add a batch name, your email and it's done! HaploFind server will send a confirmation message to the provided email address, together with the unique (and secure!) link to access your reserved area. As soon as the results are ready, we will drop you an email. By the way, you can also keep open the waiting page in your browser, and check from time to time!

What's the meaning of "SHORT", "UNK" or "ERR" codes in the haplogroup column? Or that strange cross sign in the "Complete" column?

Ooops! Well, sometimes, HaploFind has problems in the assignment. "SHORT" code means that the sequence you submitted was too short to be analyzed successfully. Remember that HaploFind is designed with complete mtDNA sequences in mind and providing sequences that are way too short may disrupt PhyloTree navigation. "UNK" means that HaploFind simply doesn't recognize any known mutational pattern. It's a rare case, it just happens if you try to submit RSRS, the new reference sequence. Since HaploFind SNP Discovery uses RSRS as its own reference sequence, obviously it will be unable to find any variant and thus any known mutational pattern. The same can happen with sequences missing the vast majority of ancient mutations for some reason.
A cross in "Complete" column means that HaploFind was able to identify the correct PhyloTree branch, but is not really sure of which subhaplogroup is the right one. Even if it's safe to ignore this error, since commonly HaploFind assignments are enough precise in any case, you can manually choose between the suggested subhaplogroups through the Tree view.
The "ERR" code is caused by errors in the pipeline that could not be recovered. Just check that your submitted FASTA file is in the correct format, and, if this is the case, please, drop us an email attaching the file or add a request in our Support&Feedback page

I need additional help! I want to give my feedback!

In this case, go straight to our Support&Feedback page! We are there waiting for you!

How to cite HaploFind?

Please cite:

    Vianello D., Sevini F., Castellani G., Lomartire L., Capri M. and Franceschi C. (2013) HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment. Hum. Mutat. doi: 10.1002/humu.22356.


HaploFind is a research tool. Altough all reasonable checks are enforced to ensure information high quality, no warranties regarding the correctness of the data are given, and we disclaim liability for damages resulting from its use.
Genetic and medical information is provided for research, informational and educational purposes only, and must not be used as a substitute for professional medical advice, diagnosis, treatment or care.

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