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 Joining or Maximum Likelihood. For this purpose we recommend Ugene which is a very powerful toolset not only for Next-Gen sequencing projects. The following steps show how simple this process can be:

1. Import your dataset as vcf, hsd or fasta into HaploGrep.

2. Export the results by clicking on the arrow next to “Save” and select Multiple Alignment Format

3. Open the downloaded file (MAF.fasta) with Ugene

4. Click on the “Build Tree” icon – also to find under ActionsTreeBuild Tree 

5. Choose the tree building method: MrBayes, PHYLIP Neighbor Joining or the PhyML Maximum Likelihood method.

6. Play around with the settings (Layout, Branch Settings, Text Formattings, Align Labels)


7. By clicking on the Camera Symbol, the tree can be exported as SVG and further edited with Inkscape


MrBayes with Jukes Cantor substitution model’s default


PhyML Max.Likelihood with JC69

 Here’s the very tiny testfile with 9 Sequences


Important to know: HaploGrep generates the multiple alignment based on the whole rCRS reference Sequence, that means even if only the Control Region (16024-576) was sequenced, the reference sequence will be used for the non-sequenced region. The filename gets extended with the haplogroup for better concordance checks.


Hansi Weissensteiner