Phylosuite

+ Fixed some bugs in MACSE, PartitionFinder, MrBayes and IQ-TREE plugins
+ Added a function to continue previous analyses for IQ-TREE and ModelFinder
+ Added a new homepage for Chinese users (http://phylosuite.jushengwu.com/)
+ Added a user-friendly partition editor for PartitionFinder and ModelFinder
+ Added an option to specify start gene for gene order figure in “Extract” function
+ Added an option to restore the settings to default
+ Updated MAFFT and IQ-TREE to newest versions

+ Updated citation for PhyloSuite
+ Added launch image
+ Changed the icon
+ Added a google group for PhyloSuite
+ Fixed a bug that caused PhyloSuite to crash when there are too large data in one workplace
+ Added shortcuts for available downstream analyses for each function (after it is finished)
+ Added context menu for each results folder to import the results into downstream functions
+ Added the option of different settings for each project
+ Added AA model for Beast to the Modelfinder analysis
+ Added an option that allows users to export/import taxonomy settings
+ Added a sorting function to Concatenation
+ Added several resources for plugins installation
+ Added a function to reorder the GenBank file
+ Added a function to change the font in PhyloSuite
+ Optimized some functions

+ Fixed a bug that caused PhyloSuite to crash on MAC and Linux
+ Added test run
+ Added strand-specific statistics to mitogenome extraction function
+ Fixed bugs in the 'Extract' function
+ Fixed a bug that caused Gblocks to crash
+ Canceled "+R" when calculating the best-fit model for BEAST
+ Added an exclusion function when customizing taxonomy recognition
+ Fixed a bug that caused incompatibility issues with MrBayes 3.2.7
+ Added rename, drag and drop functions for the file explorer in the main page of PhyloSuite
+ Added a function to extract chloroplast genome (thanks to Dr. Kai-Kai Meng)
+ Made a homepage for PhyloSuite (https://dongzhang0725.github.io)
+ Added a funtion to clear "misc_feature" in "Standardization" function
+ Fixed a bug that caused IQ-TREE and MrBayes to fail recognizing the outgroup
+ Added a function to draw a linear figure in "Concatenation"
+ Added the ability to allow mutiple results of each function, instead of overwriting them
+ Added a function to reconstruct phylogenetic trees in batches using IQ-TREE
+ Added a function to search sequences in the nucleotide and protein databases of NCBI
+ Optimized and upgraded the function of input files into PhyloSuite, see https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/five_ways_to_import/
+ Added a multi-thread MrBayes run option to the Linux version
+ Enabled the Flowchart function to save different settings as workflow
+ Allowed spaces in the software and workplace paths
+ Changed the interfaces of some functions
+ Enabled MrBayes to infer the tree at any generation
+ Enabled user to customize the sequence name when extracting sequence

+ Added test run
+ Added strand-specific statistics to mitogenome extraction function
+ Fixed bugs in the 'Extract' function
+ Fixed a bug that caused Gblocks to crash
+ Canceled "+R" when calculating the best-fit model for BEAST
+ Added an exclusion function when customizing taxonomy recognition
+ Fixed a bug that caused incompatibility issues with MrBayes 3.2.7
+ Added rename, drag and drop functions for the file explorer in the main page of PhyloSuite
+ Added a function to extract chloroplast genome (thanks to Dr. Kai-Kai Meng)
+ Made a homepage for PhyloSuite (https://dongzhang0725.github.io)
+ Added a funtion to clear "misc_feature" in "Standardization" function
+ Fixed a bug that caused IQ-TREE and MrBayes to fail recognizing the outgroup
+ Added a function to draw a linear figure in "Concatenation"
+ Added the ability to allow mutiple results of each function, instead of overwriting them
+ Added a function to reconstruct phylogenetic trees in batches using IQ-TREE
+ Added a function to search sequences in the nucleotide and protein databases of NCBI
+ Optimized and upgraded the function of input files into PhyloSuite, see https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/five_ways_to_import/
+ Added a multi-thread MrBayes run option to the Linux version
+ Enabled the Flowchart function to save different settings as workflow
+ Allowed spaces in the software and workplace paths
+ Changed the interfaces of some functions
+ Enabled MrBayes to infer the tree at any generation
+ Enabled user to customize the sequence name when extracting sequence

+ Added compiled PartitionFinder2 (MAC and Window only), which doesn't rely on Python 2.7 any more
+ Optimized plugins download and configuration, and added a demo tutorial for this (https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/how-to-configure-plugins/)
+ Fixed a bug that caused MAFFT to crash
+ Fixed bugs in "Concatenation", "Search in NCBI", and "Fasta file import" functions
+ Made a homepage for PhyloSuite (https://dongzhang0725.github.io)
+ Added a funtion to clear "misc_feature" in "Standardization" function
+ Fixed a bug that caused IQ-TREE and MrBayes to fail recognizing the outgroup
+ Added a function to draw a linear figure in "Concatenation"
+ Added the ability to allow mutiple results of each function, instead of overwriting them
+ Added a function to reconstruct phylogenetic trees in batches using IQ-TREE
+ Added a function to search sequences in the nucleotide and protein databases of NCBI
+ Optimized and upgraded the function of input files into PhyloSuite, see https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/five_ways_to_import/
+ Added a multi-thread MrBayes run option to the Linux version
+ Enabled the Flowchart function to save different settings as workflow
+ Allowed spaces in the software and workplace paths
+ Changed the interfaces of some functions
+ Enabled MrBayes to infer the tree at any generation
+ Enabled user to customize the sequence name when extracting sequence

+ Fixed the bug that caused "Flowchart" function to crash
+ Shielded the folder/files which are irrelevant to the workplace
+ Fixed the bug that caused the results of PartitionFinder to be unrecognized by MrBayes and IQ-TREE on MAC and Linux
+ Added outgroup parameters to IQ-TREE
+ Added a function to view and/or edit the command of IQ-TREE and ModelFinder before starting
+ Added a parameter to "Draw RSCU Figure" function, which can define the maximum value of y-axis
+ Fixed the bug that the child-window of PhyloSuite cannot be resized by mouse on MAC
+ Added a function to check the validity of the path of plugins, workplace and input file for each functions, and made the warning clearer
+ Added "–adjustdirectionaccurately" and "–adjustdirection" parameters to MAFFT
+ Fixed the bug that prevented the sequences to be reordered more than once in the "Concatenation" function on MAC
+ Added "Reminder settings" to "Settings-->Settings" function
+ Fixed the bug that disabled the "Continue Previous Analysis" function of MrBayes
+ Added "Default" and "Custom" options to "Extracter" function, which can extract the entire sequence and specific features, respectively