Jalview

Jalview is a handy CAD program designed to display, analyze, and track multiple sequence alignments. It’s like having a toolbox specifically for biologists and bioinformaticians!

Edit with Ease

With Jalview’s editing features, you can tweak those sequence alignments and check them out using phylogenetic trees or PCA plots. Plus, you can dive into molecular structures and annotations easily!

Open-Source Goodness

This open-source program is built on Java, making it super accessible. It works great with tools like Jmol for 3D structures and VARNA for RNA secondary structure.

A Feature-Rich Experience

The utility packs a lot of features, so you'll want to spend some time getting familiar with how everything works. No worries if you need help; there’s a detailed manual and even online video tutorials!

Flexible Workspace

You’ll notice several floating windows in the main panel. This lets you work on multiple tools all at once! You can close, minimize, or maximize them as needed. And guess what? Your current project can be saved in JAR file format so you can pick up right where you left off.

Diverse Views of Alignments

You have the option to view the same alignment in different ways at the same time! Each alignment can be ordered differently or color-coded uniquely while hiding rows and columns as needed.

Data Import & Export Made Easy

The tool allows importing or exporting data from Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR (including MODELLER variant), or Pfam/Stockholm.

Print & Save Options

You can read colored and annotated alignments from JAR files too! If you need to share your alignment view, it can be printed or saved as HTML, PNG, or EPS files.

Advanced Editing Tools

You have options to edit alignments by inserting gaps or deleting them simply by clicking your mouse or using hotkeys! There's also a cursor mode that makes keyboard editing easy—just use the space bar to add gaps!

Copying & Trimming Sequences

You’re able to copy, paste, cut or delete sequences whenever necessary. You can also undo or redo actions easily! Plus, trim your alignment left or right as needed.

Add Some Color!

Jalview comes with color schemes for nucleic sequences and fetches sequences from RFAM. You can even color parts of a sequence based on imported database records like Uniprot!

Utilize Web Services

You’ve got access to web services such as the Sequence Fetcher for retrieving sequences along with various alignment features provided by the European Bioinformatics Institute (EBI).

Calculate & Analyze Data

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