MASE

MASE (Multiple Aligned Sequence Editor) is an interactive, UNIX-based sequence alignment editor designed to couple human judgment with computational analysis for homologous nucleic acid and protein sequences. It supports simultaneous editing of large multi-sequence datasets (typically up to ~10⁶ characters total), displaying alignments in two independently scrollable windows to facilitate direct visual comparison.

The system provides an extensive library of intrinsic functions (80+), accessible via menu-driven command mode or customizable key bindings, covering cursor navigation and pattern search, insertion/deletion of alignment gaps across individual or all sequences, sequence rearrangement, and flexible display controls (e.g., highlighting conserved motifs or residue classes such as hydrophobic/hydrophilic positions). MASE can start from unaligned sequences or refine the output of external alignment programs, and it generates formatted aligned outputs with user-defined layout parameters. By integrating manual alignment operations with built-in analysis and visualization, MASE aims to improve both the efficiency and reliability of complex comparative sequence editing tasks where fully automated methods can be brittle.