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) (phylotree17_FU1.xml) is the new default tree and especially helpful for control region (HV1+HV2) sequences. The new haplogroups are marked with an asterisk “*”

New PhyloTree17_FU1 haplogroups marked with * – example of DOT export

Besides the realignment of motifs (see Dür et al 2021, Table 5¹ in ) and modified motifs (see Table S6¹), we further improved:

  • FASTA import: remove Ns from the input sample-range, so that the input range gets split and N positions are ignored from interpretation. Additionally, the FASTA import realigns insertion and deletions (indels) to match haplogroup defining motifs (by default). If you don’t want to fix the nomenclature, you can use the “–skip-alignment-rules” parameter.
  • Lineage export: generates Graphviz DOT files for graphical representation of phylogenetic tree over a sample set. See Figure 2 for example² and the Github page for more details on using this parameter.
  • Systematically check the distance between 2 haplogroups

¹Dür A, Huber N, Parson W. Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. International Journal of Molecular Sciences. 2021; 22(11):5747. https://doi.org/10.3390/ijms22115747

²Kloss-Brandstätter, A., Summerer, M., Horst, D. et al. An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Scientific Reports, 11 10816 (2021). https://doi.org/10.1038/s41598-021-90145-2

Github Project Page -> https://github.com/seppinho/haplogrep-cmd

 

Hansi Weissensteiner