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In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several European countries, Russia, and Japan, the largest set available thus far for hantaviruses.
The results show that PUUV sequences form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants is observed.
Gene/species trees reconciliation; gene duplication times in terms of speciation events; rearrange regions of a gene tree with weak support in the data to obtain alternate hypotheses Tests for significant phylogeny-trait correlations taking into account uncertainty arising from phylogenetic error by integrating over the credible set of topologies produced by a bayesian estimation method such as BEAST or Mr Bayes. A variety of special analysis tools including a test for compositional equilibrium, plotting of rate profiles along sequence alignments, and NPRS tree calibration.It also reports the deviation from the molecular clock caused by punctuational effects. Estimates median networks, parsimony splits, spectral analysis, split decomposition, neighbor-net, recombination networks, hybridization networks, standard tree reconstruction methods and the (refined) Buneman tree. It is programmable in the functional and system-independent programming language, TL.