PartFastTree: Constructing large phylogenetic trees and estimating their reliability

Darwintree: A Molecular Data Analysis and Application Environment for Phylogenetic Study

“…To promote the power of DarwinTree for phylogenetic study, several data mining tools and specific application services were developed and provided for the public. For example, the Gene Sequence Quality Control Tool(GSQCT) and its parallel implementation Cloud-GSQCT for data washing; the efficient MapReduce program for bioinformatics applications (bCloudBLAST) (Meng, Li, et al, 2011), PartFastTree, which constructs large phylogenetic trees and estimates their reliability (Li et al, 2013) and Rapidtree, which is the solution to rapid reconstruction of the phylogenetic tree (Meng et al, 2014) for improvement of bioinformatics tools; in terms of specific application tools, iDNABar, the rapid species identification toolbox for DNA barcoding collection, preservation, identification, and tracing (Meng, Zhou, Li, Gao, & Shen, 2012) and the website of information on apomixis (= apogamy) in ferns and lycophytes (Liu et al, 2012); and SoTree, Species Identification Service (SPI), the automated phylogeny assembly tool for ecologists etc. for data mining of big phylogenetic trees.…”

“…Many tools and algorithms have been used in phylogenetics to further enhance the capabilities of large data processing. However, there are still many technical problems to be solved, including data collection and screening of DNA data, automatic construction of large trees (Supertree), further excavation and sharing of information, and so on (Ciccarelli et al, 2006;Li, Meng, Hou, Zhou, & Gao, 2013;Meng, Li, et al, 2011). The following are two different ways to approach these problems: 1) integrate a number of trees into a synthetic large tree, based on the overlap of two or more smaller trees or 2) construct the TOL directly on the super-data matrix for analysis.…”