Table 1.

Troubleshooting: Some of the most common problems encountered by PhyloSuite users.

Step	Problem	Possible reason	Solutions
1.11.5 Stop the run and infer the tree function in MrBayes	Error message: could not rename file…	MrBayes is running and the file is occupied	Kill MrBayes process and try again
Multiple sequence alignment using MAFFT	The result file is empty	1. the path of the input file contains Chinese or other non‐English symbols; 2. the file contains only 1 sequence	1. replace the path of the input file with the path consisting of standard characters; 2. delete the input file with only one sequence
Could happen in different steps	Memory error	Running out of memory	Use the 64‐bit version of PhyloSuite, or run on a server with a larger memory
Saturation analysis and drawing the RSCU figure	Error message: plotlyjs argument is not a valid URL or file path	There are Chinese or other special symbols in the installation path of PhyloSuite	Install PhyloSuite to a path consisting of standard characters
In the supplementary file:get taxonomy (NCBI)	No apparent progress	The network is too slow to download the database	Try later, or manually download the “taxdump.tar.gz” file using the given url, then reopen this function and specify its path in the pop‐up window
Could happen in different steps	File input or results generation steps produce file errors	PhyloSuite does not have permission to operate the file	Assign folder permission for the installation path of PhyloSuite or the workplace folder