Sequencher

Sequencher is a Windows utility built specifically for helping users manipulate DNA sequencers and contigs.

The layout is not very intuitive and rookies may spend some trying to configure the dedicated parameters.

The application gives users the possibility to create a new project by assembling the DNA algorithms, and creating new sequence fragments and templates.

When it comes to importing files, you can drag and drop them directly into the primary panel, or use the copy and paste commands. Plus, it gives users the possibility to insert information from various file formats, namely ABI, MegaBase, CEQ, SCF, GenBank, EMBL, DDBJ and plain text files.

There are several dedicated tools designed to help you trim poor quality data or vector contamination from your sequences. This way, you can cut ambiguities and low confidence data.

Sequencher allows users to remove one sequence or multiple ones, rename a sequence or contig, automatically save the projects at preset time intervals, as well as perform basic sequence editing operations (e.g. set base numbers, find ambiguities, use voice verification to check base calls).

Plus, you can set up conditions by configuring the dedicated algorithms and parameters, opt for an automatic assembly mode, edit, move, or delete bases and sequences, insert gaps or bases, and create a new sequence from a consensus.

It is possible to analyse the differences between sequences and contigs, and it proves to be pretty useful especially for SNP analysis, mutation detection, and clone checking options.

Other important features worth mentioning enable users to view and print a report, use the chromatogram for editing the contigs, create restriction maps, find items by applying different filters, and copy the information to the Clipboard or print it.

Last but not least, the program is able to underline all ambiguous bases, highlight bases that have been edited, and you can also select a background colour, and export the information to CSM.

Sequencher comes packed with configurable DNA assembly algorithms, DNA sequence editing tools, and other useful features for helping users analyse DNA sequences and contigs in a professional way.