PhyloSuite - A New Desktop Platform Makes Phylogenetic Work Elegant
Researchers from Institute of Hydrobiology (IHB) ofChinese Academy of Sciences have developed PhyloSuite, an integrated and scalable desktop platform designed to streamline phylogenetics studies. PhyloSuite allows beginners to quick‐start their way into phylogenetic analysis, and experienced researchers to conduct, store and manage their work in a streamlined way. This work was published in Molecular Ecology Resources.
PhyloSuite was developed in Python and Qt programming languages. It integrates a number of phylogenetic and bioinformatic tools as plug-in programs, thereby streamlining the procedure normally associated with phylogenetic analyses, from data acquisition to phylogenetic tree annotation.
PhyloSuite runs on Windows, Mac OSX and Linux systems and enables users to directly search the NCBI’s Nucleotide and Protein databases. It is a user-friendly and scalable function of extraction of data from GenBank entries and a phylogenetic workflow with batch processing capability, comprising a list of plug-in software programs (MAFFT, MACSE, trimAl, HmmCleaner, PartitionFinder, MrBayes and IQ-TREE etc.).
It has automatic conversion of the output of the upstream step (program) to input for the downstream step (program) and facilitates large-scale comparative organelle genomics meta-analyses. It also stores, organizes and visualizes data and results of each analysis in the PhyloSuite workplace.
PhyloSuite has more than 26 citations since last December (comprising the published paper and the bioRxiv preprint), so it has already aided numerous comparative organellar genomic and phylogenetic studies. These studies were published in journals such as Genome Biology and Evolution, Molecular Phylogenetics and Evolution, Genomics, BMC Genomics, BMC Evolutionary Biology, BMC Plant Biology, Systematic Entomology, International Journal for Parasitology, International Journal of Biological Macromolecules, Parasites & Vectors, and so on.
“PhyloSuite looks like a very useful and easy to use GUI for phylogenetic analysis with lots of options!” commented by Bui Quang Minh, the author of IQ-TREE.
This work was supported by the National Natural Science Foundation of China (Grant No. 31872604) and the Earmarked Fund for China Agriculture Research System (Grant No. CARS-45-15).
The interface and the main functions of PhyloSuite. (Image by IHB)