HaploGrep2 Update 2.4

We are happy to provide the latest HaploGrep version 2.4. It is a major upgrade and includes an updated and revised phylogenetic tree by Dür et al 2021¹. It comes with 6,401 haplogroups – by increasing the underlying PhyloTree 17 (haplogroups n=5,435) with 966 new haplogroups. The new tree called PhylotTree 17 Forensic Update (FU) … 

 

HaploGrep2 Update 2.1.21

With HaploGrep version 2.1.21 the handling of human mitochondrial FASTA sequences gets a new improvement. As we use BWA 07.17 for the alignment of FASTA sequences, the mtDNA nomenclature is not always met by default. Therefore we provide a new parameter which will fix the nomenclature to the correct one used in Phylotree, finally yielding a … 

 

HaploGrep2 publication

Happy to announce the publication of the HaploGrep2 paper in this years Web Server Issue 2016 in Nucleic Acids Research. For data generated with massive parallel sequencing devices in form of fastq or bam files, the mtDNA-Server paper also published in this years issue, gives some details there.

 

Phylotree 17 available

After exactly 2 years, Phylotree, the “database” behind HaploGrep got updated by Mannis van Oven. Here’s the accompanying publication on Phylotree 17 . The mtDNA tree has now 5,437 haplogroups, which is a growth of over 13% to the previous version. Find out how Phylotree 17 differs for your dataset, by using the updated HaploGrep 2 … 

 

HaploGrep 2.0 is ready!

Over the last years, HaploGrep became the de facto standard for automatic haplogroup classification (~ 18.000 users, cited over 140 times, about 120 local installations) and is also used in several commercial systems and research pipelines. There was quite some work done underneath the surface of HaploGrep, especially to improve our haplogroup classification performance and … 

 

rCRS vs. RSRS vs. HG19 (Yoruba)

It’s not always straight forward when working with the human mitochondrial DNA, even if it comes to the question: “what reference sequence do you use?” There should be just one reference and the questions therefore obsolete – what however is not the case. Since the first sequencing of the human mitochondrial genome by Anderson et al. …