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 … 

 

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 … 

 

Importing VCF file to HaploGrep 2.0

With the establishment of NGS-Devices and the resulting data flood, new file formats such as FASTQ, SAM, BAM or VCF became de-facto standards in the bioinformatics data world. Especially the VCF-file containing the variants became of special interest in the user requests lately. There are some python scripts available, that convert a VCF file to a … 

 

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. …