There are many bioinformatics tools available to help analyze and interpret large-scale molecular data generated from crop research. Some commonly used tools include: Genome assemblers, Alignment tools, Transcriptome assemblers, Differential expression analysis tools, Variant callers, Gene ontology analysis tools, Pathway analysis tools....

I highly recommend you to focus on your education and understanding the basics and fundamentals and not to spam here by posting questions and answering yourself.

Further, since you don't have the proper education to understand what software can be used for what it is totally illogical to talk about bioinformatics tools.

Have a look here: https://bioconductor.org/

There are several bioinformatics tools available to analyze and interpret large-scale molecular data generated from crop research. Here are some commonly used tools:

These are just a few examples of the many bioinformatics tools available for analyzing and interpreting large-scale molecular data in crop research. The choice of tools depends on the specific analysis goals and data types involved in the study.