HaploGrep 2 Stand-alone Version

With some delay, we finally updated the stand-alone Version of HaploGrep to the latest version 2. This includes the latest Phylotree 17 (Forensic Science International: Genetics Supplement Series, from December 2015), finescaling the human phylogeny even further. This version has no file-upload limit as  currently applied on the web service (file size of 5MB and … 

 

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 … 

 

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’s RestAPI now available!

Hi all, due to many requests we are happy to announce that we provide Haplogrep’s REST API to the public! This will allow everyone to determine haplogroups in a very convenient way. In the following snippets we show how a simple call works (a) from the UNIX command line using curl and (b) from Java. If you … 

 

1000G Phase 3 mtDNA data available

The 1000 Genome Consortium recently released the Phase 3 mitochondrial DNA data of over 2,500 samples for download, besides their papers in Nature, stating: Mitochondrial chromosome variants are now available for the Phase 3 individuals from our FTP site Since in the current Version HaploGrep 2 can deal with the VCF file (unzipped), all 2500 … 

 

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 … 

 

NGS, HaploGrep and Hadoop MapReduce

Many of our HaploGrep users are interested in analysing data within automated pipelines. To support users with a scalable and standardized service, we are happy to present you our newest project, called mtDNA-Server. mtDNA-Server provides a free service for the complete workflow of NGS mtDNA projects. It includes the alignment of FASTQ SE/PE data based … 

 

New Feature: Tree-based visualisation of haplogroups

Within the new HaploGrep 2.0 Beta version some new export formats are now supported. One of the most powerful is the export of a phylogenetic tree, representing the current profiles loaded into HaploGrep. This feature generates almost publication-ready  phylogenetic trees. We used them with almost no modification (some color-highlighting in Inkscape) – please see [1]. Click here to … 

 

HaploGrep 2.0 – Beta

We are happy to announce HaploGrep 2.0 – Beta Version. We want YOU to give it a try, and help us to improve the software. We also want to say thanks to all the fruitful discussions, especially with our collaborators Antonio Salas and Hans Bandelt. All new features will be introduced one by one in …