SoTree: An Automated Phylogeny Assembly Tool for Ecologists from Big Tree

Entire areas of study, such as community phylogenetics and comparative analysis, require detailed phylogenetic, as well as ecological information. China has 31,362 species of vascular plants belonging to 3,328 genera and 312 families, which is ranked in the top six megadiverse countries of the world. along with the big tree of vascular plants in China has been completed recently, SoTree, an automated phylogeny assembly tool is being implemented for ecologists. This paper presents SoTree to the big tree of vascular plants in China for ecologists to generate a phylogeny by search species from an excellent genus-level reference phylogeny on the basis of taxonomy. Meanwhile, the algorithm and solution of SoTree is also described which is based on several steps including parsing, reconstructing and storing of the Basic big phylogenetic tree, standardization of species sub-list, retrieving each node element in the chain, construction of group relation of node elements, calculation weight of each element, assembly of output phylogenetic tree and visualization of this phylogenetic tree in a web interactive environment. SoTree is an online phylogenetic query tool where users submit a list of taxa (e.g. from an ecological community), with genus and species names, get a phylogenetic hypothesis for the relationships among taxa and then can do visualization for trees (phylogenetic tree, time tree or both). Several input ways can be used and several output formats for tree can be selected, while any name will be marked at the accepted name or synonym according to Flora of China (FOC). Therfore, Ecologists can get accurate tree data and save a lot of time and effort. Currently, the source databases cover vascular plants. SoTree is prepared at the URL: http://www.darwintree.cn/flora/index.shtml.