Phyloqon: a tool for accurate phylogenetic tree reconstruction from quartets

Abstract

Evolution and the reconstruction of phylogenetic tree or phylogeny reconstruction are classical topics in biology. Various computational techniques have been applied in the computational biology literature for phylogeny reconstruction. One such method, quartet-based phylogenetic tree reconstruction method, has been accepting broad consideration over than last few years. Quartet is assumed to be the most basic information unit in the context of phylogeny and is an unrooted tree having 4 (four) taxa. The goal is to combine a set of quartets into a single tree that can represent the evolutionary relation of all the species in the entire set of quartets. The most recent and high-flying quartet-based phylogenetic tree reconstruction approaches are, Quartet Max-Cut (QMC) [1], Quartet FM (QFM) [2] and SVDquartets [3]. Reconstruction based phylogenetic tree visualization tools has became very essential and desirable subjects for biological research. There are large numbers of phylogenetic tree vizualization tool available, some are web-based and some are desktop based. Most of the them visualize already constructed phylogenetic tree, that means a tool takes a already constructed phylogenetic tree as input and visualise that tree in different format. Very few number of tools are available which construct, visualise and analyze phylogenetic trees, but the situation is, all of them are using sequence-based method to reconstruct the trees.

We have developed a web-based tool PhyloQon which can construct, visualise and analyze phylogenetic trees using quartet-based methods. We incorporate QFM, QMC and SVDquartets approaches to reconstruct the trees, where QFM and QMC both take a set of quartets as input and construct phylogenetic tree, but the format of the quratets are different. QFM takes input quartets in Newick format and constructs a unrooted phylogenetic tree as output. SVDquartets takes sequences as input in PHYLIP format, and it only generates a set of quartets as output. Next, it applies QFM or QMC for reconstructing the phylogenetic tree and recommends QMC or QFM for better result. Our developed tool has also integrated with another option for taking

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input, is gene tree. Several tree visualization options (i.e. circular and/or rectangular pattern) for viewing the constructed phylogenetic trees are available. Very few number of tools are available, that can visualise more than one trees at a same view. In our tool we have facilities to reconstruct trees with single or multiple approaches and also view them side-by-side. It will help the users to visually compare the trees which are constructed using different approaches with same input datasets. User can also import data and export data and graphical view of the constructed trees. We have developed an API of this tool, which enables us to get the data without using the graphical user interface of the web page.