For comparative genomics, particularly when dealing with plasmid typing and mapping in the context of horizontal gene transfer (HGT) of antibiotic resistance, there are several alternative tools to Mauve and Easyfig that you can consider. These tools vary in their functionalities, from genome alignment to visualization and analysis. Here are some alternatives:

Tips for Troubleshooting Easyfig:

• BLAST Issues: Ensure that NCBI BLAST is correctly installed on your system. Sometimes, manually installing and configuring BLAST can resolve issues that arise with automatic installations.
• Compatibility: Check if your version of Easyfig is compatible with your operating system and the versions of other software it interacts with.

Considerations:

• Choice of Tool: The choice of tool depends on your specific requirements, such as the level of detail needed, ease of use, and the scale of your comparative analysis.
• Learning Curve: Some tools have a steeper learning curve but offer more functionalities. Consider the time investment required to learn each tool.
• Data Privacy: If working with sensitive data, consider the data privacy policies of each tool, especially web-based tools.

Remember, in bioinformatics, it's often beneficial to try multiple tools to determine which best suits your specific project needs.

Hope i have addressed your concern. feel free to ask your question.

Best,

Dr. Pri