Linear or circular contigs can be assembled de novo from overlapping sequences or Sanger sequence traces.

Sequences to be aligned can now be imported in various ways. A portion of a multiple alignment can be extracted to generate a new multiple alignment, or an existing multiple alignment can be edited to add or remove alignments generated by different algorithms.

Nicking endonucleases can be displayed. When a selection spans from an end of a linear sequence to a nicking endonuclease site, that single-stranded region can be removed by pressing Delete.

Zero-length point features are now supported for DNA sequences, and are recognized when importing files from GenBank, MacVector, or Gene Construction Kit.

Commonly used enzyme sites can be highlighted in gold for quick identification.

Consensus sequences for multiple alignments have an improved format, and can now be copied or exported.

By popular demand, when an alignment to a reference DNA sequence is edited by adjusting the endpoints of the aligned sequences, those edits are preserved and restored.

Features can be imported into a DNA sequence from BED, GFF3, or GTF formats.

Protein sequence records can be imported from the UniProt database.

When a primer is added to a file, the date is recorded. Primers can be sorted by Date Added.