Mitochondrial DNA haplogroup detection software tools | Phylogenomics data analysis
The determination of human mitochondrial DNA (mtDNA) haplogroups is not only crucial in anthropological and forensic studies, but is also helpful in the medical field to prevent establishment of wrong disease associations. In recent years, high-throughput technologies and the huge amounts of data they create, as well as the regular updates to the mtDNA phylogenetic tree, mean that there is a need for an automated approach which can make a speedier determination of haplogroups than can be made by using the traditional manual method.
Identifies haplogroups by traversing the underlying phylogenetic tree Phylotree. HaploGrep is able to support high quality mitochondrial DNA (mtDNA) research projects with a profound quality control (QC). It enables detection of artificial recombination. This tool provides a recombination strategy that assumes prior knowledge about the specific placement of the fragments of the polymerase chain reaction (PCR) products (amplicons).
Provides a convenient, user-friendly interface for handling human mtDNA sequence data. It contains multiple modules which cover a wide array of functions: (i) to automatically yield a list of the variants in certain mtDNA relative to the revised Cambridge Reference Sequence (rCRS) recommended or the Reconstructed Sapiens Reference Sequence (RSRS) and determine the haplogroup status of that lineage according to Phylotree (www.phylotree.org), (ii) to detect missing sequence variants in certain mtDNA with claimed haplogroup status, (iii) to display the location of the variant, interspecies conservation index and change of amino acid status, (iv) to identify potentially pathogenic mutations based on the reported data, (v) to conduct statistical analysis for haplogroup distribution frequency between case and control groups, and (vi) to retrieve and batch download analytical output and mitochondrion-related data of interest.
A pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases.
Provides a mitochondrial DNA haplogroup prediction method. H-mito is an application based on the phylogenetic tree. It can be used: (i) if users already have the mutation lists for sequences, (ii) if users only have the alignment of sequences to the reference, or (iii) if users only have the sequences. This method also includes ancillary scripts to extract mutation lists and to join, align through clustalW and convert data.
A mitochondrial genome haplogroup-defining algorithm using a k-mer approach. Phy-Mer performs equally well as the leading haplogroup classifier, HaploGrep, while avoiding the errors that may occur when preparing variants to required formats and notations.
Provides an automated comparison method for human mitochondrial DNA (mtDNA). mtDNAoffice determines distances between mtDNA sequences allowing their subsequent clustering and haplogroup assignment that may increase the speed of data analysis and avoid human errors. This software also allows users to extract mtDNA regions, select sequences with specific characteristics and download sequences from online databases.
Permits high-throughput classification of European, African, and Native American mitochondrial haplogroup lineages. Hi-MC uses a defined panel of mitochondrial single nucleotide polymorphisms (SNPs) for classification of mitochondrial haplogroups eliminating the need for time-consuming SNP selection. Moreover, it offers an algorithm that leverages a validated human mitochondrial DNA (mtDNA) SNP panel for mitochondrial haplogroup classification and is particularly valuable for studies in which sequencing is not feasible.