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.
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.
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.
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
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.