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Updated: May 24, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.

Conan K Wang¹, Ursula Broder, Saroja K Weeratunga

¹Structural Chemistry Program, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Qld 4111, Australia. conan.wang@griffith.edu.au

Bioinformatics (Oxford, England)

|February 15, 2012

Summary

We developed SBAL, a user-friendly tool for generating and visualizing secondary structure-based sequence alignments. This software offers automated and semi-automated approaches comparable to existing tools, enhancing biological data analysis.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Generating biologically meaningful sequence alignments requires both alignment and visualization.
Existing computational tools often lack integrated, user-friendly approaches for secondary structure-based alignments.
There is a need for software that combines reliable automated and semi-automated methods with effective visualization.

Purpose of the Study:

To develop SBAL, a novel tool for generating and editing secondary structure-based sequence alignments.
To provide a user-friendly interface for visualizing sequence alignments with mapped secondary structure information.
To offer an algorithm for automated and semi-automated alignment calculations with performance comparable to existing software.

Main Methods:

SBAL is implemented in Java for cross-platform compatibility.
It utilizes a simple color scheme to map secondary structure assignments to sequence regions.
The tool supports both automated and semi-automated alignment generation.

Main Results:

SBAL provides a user-friendly interface for generating and editing secondary structure-based sequence alignments.
The visualization feature maps secondary structure assignments to sequences using color coding.
The implemented algorithm demonstrates performance comparable to established software.

Conclusions:

SBAL is an easy-to-install tool that facilitates the creation and editing of biologically meaningful sequence alignments.
The software effectively visualizes secondary structure information alongside sequence alignments.
SBAL offers a valuable computational resource for researchers in bioinformatics and structural biology.