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Updated: May 6, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PRALINE: a versatile multiple sequence alignment toolkit.

Punto Bawono¹, Jaap Heringa

¹Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|October 31, 2013

Summary

This summary is machine-generated.

Profile Alignment (PRALINE) is a versatile toolkit for protein multiple sequence alignment. It offers various optimization strategies and visualization tools for interpreting and publishing sequence relationships.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Multiple sequence alignment is crucial for understanding protein function and evolution.
Existing tools may lack flexibility in handling diverse alignment challenges.

Purpose of the Study:

To introduce Profile Alignment (PRALINE), a comprehensive toolkit for protein multiple sequence alignment.
To highlight PRALINE's advanced optimization strategies and user-friendly online server.

Main Methods:

PRALINE employs a global progressive alignment algorithm.
It integrates strategies like profile preprocessing, homology extension, secondary structure guidance, and transmembrane awareness.
The toolkit offers combinations of these strategies for tailored alignments.

Main Results:

PRALINE provides an accessible online server with extensive visualization capabilities.
Generated alignments can be exported in PDF format for publication.
Sequence relationships are visualized using dendrograms.

Conclusions:

PRALINE is a versatile and powerful tool for protein multiple sequence alignment.
Its advanced features and visualization options aid in interpreting and publishing biological sequence data.