SeqFIRE prep is for users who want to run SeqFIRE with a large amount of data (several sequence alignments). We provide a batch mode analysis option for both indel region and conserved block modules. In order to use the batch mode, first prepare the input files in a SeqFIRE compatible format. For this, we provide a small Python script called SeqFIREprep. SeqFIREprep will merge multiple alignment files into a single large input file. The script can also be used for subsequent separation of the results into separate output files for each alignment.
SeqFIRE standalone is for users who want to run SeqFIRE on a standalone computer or a local server.