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 … 

 

New HaploGrep Exports in Detail

Here’s the overview of the new export options, HaploGrep 2 offers, by clicking on the small arrow next to Export: a) The HaploGrep result file as default format, ending with .HSD – find out more about the simple text-format, as well as an Example file. b) The extended HaploGrep result file, with remaining and not … 

 

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 … 

 

HaploGrep Export Formats for Phylogenetic trees

HaploGrep 2.0 Beta allows the export of a multiple alignment fasta format. Working with the new version, the generation of phylogenetic trees becomes therefore straight forward. Beside its own Phylogenetic tree directly based on Phylotree (see previous blog entry), we present here the basic steps to generate phylogenetic trees based on multiple alignment fasta files by using MrBayes, Neighbor …