FasParser is a graphical platform for manipulating sequences and alignments in a batch mode. It is particularly useful for biologists handling large datasets of sequences, even without an experience in programming. Here, I present an updated version FasParser2, featuring numerous improvements with sets of novel functions that can facilitate sequence manipulation. Its main additional features include (i) re-designed graphical interface which greatly improves its capability for batch processing, (ii) a trimming function to strip poorly-aligned regions in multiple sequence alignments, (iii) a series of functions that can identify as well as remove bad sequence (either too short or too divergent sequences), (iv) an Editor tool for viewing and editing of biological sequences and (v) interfaces (with other programs) for detection of positive selection as well as primer design.