Fasta Converter

Fasta Converter identifies all FASTA files in a specified directory and joins them into a single file. This is a feather-light application whose options are intuitive enough even for less experienced users. It doesn't require installation.
Before proceeding any further, you should know that Fasta Converter is a pretty old program. It still runs on newer Windows editions but has compatibility issues.

Plain and simple interface

It's wrapped in a simple interface made from a large window with three panes which let you select a directory, view files, and examine file contents. Any drive can be selected from a drop-down menu to explore its directories, whether it's local, removable, mounted, or in the network.

Merge FASTA files using three methods

By default, the program shows all forms of FASTA file types in the folder, and they can be filtered by FSA, FA, FAS, FASTA or FST format. Two or more files can be selected for the merging procedure, which automatically generates the output file in the same location as the source (this option cannot be changed).
There are three ways to merge the files: the standard mode creates standard MultiFast files as they are, the renamed mode instructs the utility to replace the internal comments with the file names, while compact mode strips the files of their comments.

Evaluation and conclusion

It carried out merging jobs swiftly in our tests while remaining light on system resources consumption. Unfortunately, although this outdated tool still runs on later Windows versions, it froze and crashed whenever we attempted to view a file's content or to merge files.
To conclude, Fasta Converter offers a simple solution for joining together FASTA files using three methods available, provided that you are running a Windows version that's no longer officially supported by Microsoft.