PhyloSuite

Examples

All examples can be found in example folder of the PhyloSuite root folder or downloaded from https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/example.zip or http://phylosuite.jushengwu.com/example.zip (China).

Test run

1. PhyloSuite installation

Please see https://dongzhang0725.github.io/dongzhang0725.github.io/installation/.

2. Install plugins

Please see https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/how-to-configure-plugins/.

3. Run the test

Here I use 31 marine turtle mitogenomes as an example. For the original paper see https://www.sciencedirect.com/science/article/pii/S1055790312002242#t0005.

3.1 Import mitogenomes

  1. Select any of the work folders (here I chose files);
  2. Click Open file(s)/Input ID(s) to open the input window;
  3. Click Choose Files in the Input by files box;
  4. Go to PhyloSuite root folder, open the tests folder, then choose marine_turtle_mitogenomes.gb;
  5. Click Open to import.

3.2 Gene extraction

  1. In the main interface, choose files work folder, select all sequences;
  2. Right-click and choose Extract to enter the extraction interface;
  3. Select the predefined Mitogenome as the sequence type;
  4. Select 2 Vertebrate mitochondrial code;
  5. Click to rename the output dir name as test_run;
  6. Click Start to extract.

3.3 Phylogenetic workflow

3.3.1 Choose workflow
  1. Click Flowchart in the menu bar;
  2. Choose Test run in the Workflow menu;
3.3.2 Input file and parameter setting

  1. Only the first program needs an input file, so click the red Input file here to open the MAFFT program window;

  2. Click the file input box of MAFFT to view the automatically prepared input files (you may opt to use a different file via No, thanks);

  3. Select the results that you extracted in section 3.2 (test_run in extract_results);

  4. Click Ok to import.

  5. Tick Extract-Seq option and then tick PCGs, and the nucleotide sequences of protein-coding genes will be imported automatically;

  6. To speed up the test, you may pop-up the files menu and remove all files but ‘nad3.fas’, ‘nad4L.fas’ and ‘nad6.fas’ files (using the remove button [red x sign]);

  7. Select 2 Vertebrate mitochondrial code;

  8. Just close the window to save the imported files and parameters.

3.3.3 Start workflow
  1. Click the Check | Start button, and the parameter summary window will pop up, allowing you to check and modify the parameters;
  2. Click Ok, start to start the workflow.
3.3.4 Get workflow results

When all the tasks are finished, click Ok to view the results, double-click the folders in the list of results box to open the corresponding results:

Scroll to the bottom of the results, and you will see that the whole workflow takes around 3 minutes (CPU: AMD Ryzen 7 1700; RAM: 8 G; OS: Windows 10 64 bit).

Note: to make this ‘test run’ very fast, I set a very low number of generations for MrBayes (10000) and IQ-TREE ultrafast bootstrap (5000).

4. Test run of each function

You may view a brief demo and/or test for each function via the inbuilt question mark button. For example:

Other demo tutorials can be found here.