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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Updated: Sep 29, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments.

Charlotte Tumescheit¹, Andrew E Firth¹, Katherine Brown¹

¹Department of Pathology, University of Cambridge, Cambridge, United Kingdom.

|March 21, 2022

Summary

This summary is machine-generated.

A new tool, CIAlign, automatically cleans multiple sequence alignments (MSAs) by removing gaps, divergent sequences, and poorly aligned ends. This user-friendly software improves bioinformatics analyses and offers clear visualizations of processed alignments.

Keywords:

Alignment quality Comparative genomics Multiple sequence alignment Phylogenetics Python tool Transcriptomics

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Last Updated: Sep 29, 2025

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignments (MSAs) are fundamental in biological research for analyzing sequence features and relationships.
Common issues in MSAs include incomplete sequences, high divergence, large gaps, insertions, deletions, and poorly aligned ends, which can hinder analysis accuracy and speed.
Manual MSA editing is prevalent but is labor-intensive and lacks reproducibility.

Purpose of the Study:

To develop a user-friendly and comprehensive tool for automated multiple sequence alignment (MSA) trimming.
To provide users with customizable options for cleaning MSAs and enhancing the transparency of the process.
To offer novel visualization features for improved understanding of alignment processing.

Main Methods:

Developed CIAlign, a command-line tool for MSA trimming with multiple customizable options.
Implemented functionalities to remove gaps, low-coverage regions (insertions), divergent/short sequences, and poorly aligned ends.
Integrated graphical output to visualize alignments before and after processing.

Main Results:

CIAlign effectively removes problematic regions and sequences from MSAs.
The tool offers customizable parameters for tailored alignment cleaning.
Novel visualization options provide clear insights into the trimming process.

Conclusions:

CIAlign provides an efficient and transparent solution for automated MSA cleaning.
The tool enhances the quality of MSAs for downstream bioinformatics analyses.
CIAlign is valuable for researchers needing to refine alignments and visualize large datasets.