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Following are partial list of bioinformatics tools, in alpha-betic order: This tool allows users to explore the characteristics of amino acids by comparing their structural and chemical properties, predicting protein sequence changes caused by mutations, viewing common substitutions, and browsing the functions of given residues in conserved domains.

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The Assembly Viewer allows a user to see the multiple sequence alignments as well as the actual sequence chromatogram.

Finds regions of local similarity between biological sequences.

The first algorithm is designed for short queries up to ~200bp with low error rate (A stand-alone application for classifying protein sequences and investigating their evolutionary relationships.

CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own.

CDTree is tightly integrated with Entrez CDD and Cn3D, and allows users to create and update protein domain alignments.

COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.

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