mtPhyl - software tool for human mtDNA analysis and phylogeny reconstruction

mtPhyl was initially designed to compare any mtDNA sequence or set of sequences with rCRS (Andrews, et al., 1999) and then to export the results into Excel format. Subsequently, additional functions have been integrated. Current version of mtPhyl can perform different types of searches; analyze mutation features; export list of mutations in particular mtDNAs into Excel table; define mitochondrial haplotype; reconstruct maximum parsimony phylogenetic tree; calculate coalescence time of clusters; calculate the effect of natural selection; make reference list; download human mtDNA complete sequences from the GenBank.

 The user communicates with mtPhyl using a menu-driven interface. DNA sequence is entered in a standard FASTA format or from “.txt” files containing partial or complete nucleotide sequence.

With mtPhyl user can perform different types of searches. For example search of sequences which contain (or do not contain) particular mutation or search of identical or similar DNAs. User may easily edit mtDNA sequences with a user-friendly DNA editing tool.

Analysis of mutation properties is performed with an integrated MutaAnalyzer miniprogram, which identifies the affected region/gene and assigns the conservation index (CI, Ruiz-Pesini et al. 2004) to the aminoacid residues.

 mtPhyl can reconstruct maximum parsimony phylogenetic trees and to process them into Microsoft PowerPoint or Excel formats and into standard Newick format. mtPhyl calculates haplogroup divergence estimate ρ and its error range as average of the distances from the tips to the most recent common ancestor of the haplogroup (Morral, et al., 1994; Saillard, et al., 2000) using different mutation rates (Forster, et al., 1996; Kivisild, et al., 2006; Mishmar, et al., 2003). Large trees, which do not fit one page, can be shown in a printer-friendly version. Additionally, user may specify mutations which will not be used in phylogenetic tree reconstruction. Since there are intense debates about mitochondrial haplogroup nomenclature (see van Oven and Kayser, 2008 and references therein), user may stick to a preferred one by changing the haplogroup name in HaploGroup.txt file.

 mtPhyl can also perform neutrality tests (Elson, et al., 2004; Ruiz-Pesini, et al., 2004) and extract references for the sequences analyzed.