mtPhyl

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 useful functions have been integrated. Current version of mtPhyl can execute the following tasks: it performs different types of searches; analyzes mutation features; exports list of mutations in particular mtDNAs into Excel table; defines mitochondrial haplotype; reconstructs maximum parsimony phylogenetic tree; calculates coalescence time of clusters; calculates the effect of natural selection; makes reference list; downloads human mtDNA complete sequences from 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 for 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.

Moreover, mtPhyl is designed to reconstruct maximum parsimony phylogenetic trees and to process them into Microsoft PowerPoint graphic format and in standard Newick format. mtPhyl calculates haplogroup divergence estimates ρ and their error ranges as averages 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 for 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 nomenclature 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.

Andrews, R.M., Kubacka, I., Chinnery, P.F., Lightowlers, R.N., Turnbull, D.M. and Howell, N. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat Genet, 23, 147.

Elson, J.L., Turnbull, D.M. and Howell, N. (2004) Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection, Am J Hum Genet, 74, 229-238.

Forster, P., Harding, R., Torroni, A. and Bandelt, H.J. (1996) Origin and evolution of Native American mtDNA variation: a reappraisal, Am J Hum Genet, 59, 935-945.

Hedges, S.B. (2000) Human evolution. A start for population genomics, Nature, 408, 652-653.

Kivisild, T., Shen, P., Wall, D.P., Do, B., Sung, R., Davis, K., Passarino, G., Underhill, P.A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knijff, P., Feldman, M., Cavalli-Sforza, L.L. and Oefner, P.J. (2006) The role of selection in the evolution of human mitochondrial genomes, Genetics, 172, 373-387.

Mishmar, D., Ruiz-Pesini, E., Golik, P., Macaulay, V., Clark, A.G., Hosseini, S., Brandon, M., Easley, K., Chen, E., Brown, M.D., Sukernik, R.I., Olckers, A. and Wallace, D.C. (2003) Natural selection shaped regional mtDNA variation in humans, Proc Natl Acad Sci U S A, 100, 171-176.

Morral, N., Bertranpetit, J., Estivill, X., Nunes, V., Casals, T., Gimenez, J., Reis, A., Varon-Mateeva, R., Macek, M., Jr., Kalaydjieva, L. and et al. (1994) The origin of the major cystic fibrosis mutation (delta F508) in European populations, Nat Genet, 7, 169-175.

Ruiz-Pesini, E., Mishmar, D., Brandon, M., Procaccio, V. and Wallace, D.C. (2004) Effects of purifying and adaptive selection on regional variation in human mtDNA, Science, 303, 223-226.

van Oven, M. and Kayser, M. (2008) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum Mutat.

   mtPhyl v.2.90

   mtPhyl v 3.00 - this is a demo version. To get full version, please contact us (eltsovnp@mail.ru or  eltsovn@gmail.com). If you didn't get a reply, please repeat your message to another e-mail.