TY  - JOUR
T1  - PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
AU  - Zhang, Dong
AU  - Gao, Fangluan
AU  - Jakovlić, Ivan
AU  - Zou, Hong
AU  - Zhang, Jin
AU  - Li, Wen X.
AU  - Wang, Gui T.
Y1  - 2020/01/01
PY  - 2020
DA  - 2020/01/01
N1  - doi: 10.1111/1755-0998.13096
DO  - 10.1111/1755-0998.13096
T2  - Molecular Ecology Resources
JF  - Molecular Ecology Resources
JO  - Molecular Ecology Resources
JA  - Mol Ecol Resour
SP  - 348
EP  - 355
VL  - 20
IS  - 1
KW  - batch capacity
KW  - GenBank extraction
KW  - high efficiency
KW  - multicore operation
KW  - partition analysis
KW  - phylogenetic flowchart
PB  - John Wiley & Sons, Ltd (10.1111)
SN  - 1755-098X
M3  - doi: 10.1111/1755-0998.13096
UR  - https://doi.org/10.1111/1755-0998.13096
Y2  - 2020/01/03
N2  - 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.
ER  -