Does anybody know how to convert .scf file (chromatogram file) to .fsa format?
You need this for Linux or Windows platform?
On Windows DNA Baser Assembler can do the conversion. There is a tool included in that package that can also do BATCH conversion.
It's likely that this earlier thread will prove helpful: How to convert and filter SCF format into Fasta?. The short answer would be to look into the staden package.