Protein Alignment

To compare two or more protein sequences, paste sequences or import FASTA files and click Run Alignment.

100% local processing. All alignments run entirely in your browser using plain JavaScript. No sequence data is ever transmitted, uploaded, or sent to any server or third-party service.

1. Sequences

2. Alignment Options

Chain type CDR scheme

Annotate CDR regions

Alignment mode

Local (Smith-Waterman) Global (Needleman-Wunsch)

Gap open Gap extend

CDR annotation is built-in - no external packages needed. Kabat anchors are reliable for human/humanized VH, Vk, and Vl sequences.