PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

Abstract

Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time‐consuming and tedious. Here, we present PhyloSuite, a (cross‐platform, open‐source, stand‐alone Python graphical user interface) user‐friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin‐based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point‐and‐click and drag‐and‐drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq‐tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick‐start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.

Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)

“…Nucleotide composition, composition skew, codon usage, relative synonymous codon using (RSCU), and architecture tables were calculated by PhyloSuite v 1.2.1 [36]. The tandem repeats of the A+T-rich region were established by Tandem Repeats Finder Online server (http://tandem.bu.…”

“…Gblocks v 0.91b was used to remove gaps and ambiguous sites [43]. Aligned PCGs and rRNAs were concatenated by PhyloSuite respectively [36]. Based on previous studies, 13PCGs and two rRNAs were widely used to construct a phylogenetic relationship.…”

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

“…The mitogenomes were obtained on 24 September 2019, from NCBI GenBank (Available online: http://www.ncbi.nlm.nih.gov). All mitogenome sequences were imported and standardized in PhyloSuite [57]. All PCGs, tRNAs, and rRNAs were extracted and aligned with MAFFT [58].…”

The complete mitochondrial genome of Scolytus schevyrewi Semenov (Coleoptera: Curculionidae)

“…The MrBayes molecular phylogeny shown in Figure 1 is based on the 13 PCGs, 22tRNAs, and 2 rRNAs of S. schevyrewi and 8 other Scolytinae beetles is constructed using PhyloSuite (Ronquist et al 2012;Katoh and Standley 2013;Lanfear et al, 2016;Zhang et al 2019), Hylobius abietis and Brachytemnus porcatusare used as outgroups. This phylogenetic tree is similar to the phylogenetic tree of IQ-tree analysis (Nguyen et al 2015).…”