Quick start

Chinese homepage link: http://phylosuite.jushengwu.com/

1. Installation

1.1 PhyloSuite

Please see http://phylosuite.jushengwu.com/dongzhang0725.github.io/installation/.

1.2 Plugins

Please see http://phylosuite.jushengwu.com/dongzhang0725.github.io/PhyloSuite-demo/how-to-configure-plugins/.

2. Operation

For the basic operation of PhyloSuite, please see http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#4-1-0-1-Brief-example.

3. Create a workplace

When starting a new project, it’s recommended to create a new workplace for it.

  1. Hovering over WorkPlace menu bar will popup available workplaces, select Others to open the Set workplace window;
  2. Click add button to select a workplace folder.

4. Create a work folder

Work folders are where you can deposit input data and results for different analyses.

  1. Click the green add button;
  2. Enter the new work folder name.

5. Import sequences

Please see five ways to import sequences into PhyloSuite.

6. Start the analysis

6.1. Examples and test run

Please see http://phylosuite.jushengwu.com/dongzhang0725.github.io/example/

6.2. Example of each function

You can access a brief example demo of each function via the question mark button in the window of the corresponding function. For example:

6.3. Comprehensive demo tutorials

For comprehensive tutorials for different analyses, please see single-gene tutorial and muti-gene tutorial.

7. Get the results

7.1. Select a work folder

By default, if you select a work folder or a results folder in a work folder before opening the function window, the results will be deposited in the selected work folder. Otherwise, the results will be deposited in GenBank_File/files or Other_File/files work folder. You can select a work folder via the ‘down arrow’ menu of the Start button in each function.

7.2. Set the output directory name

Starting with the version 1.1.15, PhyloSuite allows results of multiple analyses to be stored within each results folder in different output directories within a single Results folder. The default format of the directory name is: year_month_day-hour_minute_second, but you can change it according to your preferences.

7.3. Delete results

You can remove results you don’t need any more through the Remove function, accessed via the right-click menu.

However, we recommend to remove them in your local file system, as that will enable you to recover them using the inbuilt operating system file recovery function. You can enter the local file system via the Open in file explorer option (see the figure above).

Other demo tutorials can be seen here.