Clustal X

Clustal X

Clustal X is a free software tool for multiple sequence alignment of proteins and DNA. It allows easy alignment of sequences and analysis of alignments with interactive graphics. It is commonly used for phylogenetics and sequence analysis.
Science & Education Bioinformatics
multiple-sequence-alignment phylogenetics dna-alignment protein-alignment
Clustal X alternatives ➤

Clustal X: Free Multiple Sequence Alignment Tool

Free software tool for protein & DNA sequence alignment, with interactive graphics and analysis capabilities, commonly used in phylogenetics and sequence analysis.

What is Clustal X?

Clustal X is a widely used software tool for multiple sequence alignment of both DNA and proteins. It was first released in 2000 as a graphical user interface frontend for the command line Clustal W software. Clustal X provides an easy-to-use graphical interface that allows users to align sequences and analyze the alignments through interactive graphics and dendrogram trees.

Some key features of Clustal X include:

  • Ability to align large numbers of sequences
  • Various alignment parameters to adjust gap opening and extension penalties
  • Analyze alignments with percent identity matrices and dendrogram phylogeny trees
  • Interactive graphics allow easy analysis of alignment quality
  • Save alignments in a variety of formats for further analysis

Clustal X has been widely adopted by molecular biologists for applications such as phylogenetic analysis, sequence analysis, and identification of conserved domains or motifs. While newer and more sophisticated alignment algorithms have been developed, Clustal X remains a useful and accessible tool for basic sequence alignment tasks especially for those without advanced computational skills.

The software is no longer actively maintained and has largely been superseded by web-based tools like Clustal Omega or command line tools like Clustal W or MUSCLE. However, Clustal X still provides a straightforward GUI option for sequence alignment and analysis on local desktop machines.

Clustal X Features

Features

  1. Multiple sequence alignment
  2. Phylogeny reconstruction
  3. Interactive graphics and analysis
  4. User-friendly graphical user interface
  5. Support for large datasets

Pricing

  • Free
  • Open Source

Pros

Free and open source

Easy to use interface

Fast computation of alignments

Wide range of alignment parameters

Good for beginners

Cons

Limited alignment accuracy with divergent sequences

Does not scale well for very large datasets

Lacks some advanced features of paid aligners

Development discontinued in 2012

Official Links

Official Website
https://www.clustal.org/clustal2/

The Best Clustal X Alternatives

Top Science & Education and Bioinformatics and other similar apps like Clustal X

Here are some alternatives to Clustal X:

BioEdit icon
BioEdit
Geneious icon
Geneious
Vector NTI icon
Vector NTI
Clustal Omega icon
Clustal Omega
CLC Main Workbench icon
CLC Main Workbench
GeneDoc icon
GeneDoc
Suggest an alternative ❐

BioEdit icon

BioEdit

BioEdit is a versatile biological sequence alignment editor and analysis software for Windows. First released in 1997 by Tom Hall, BioEdit has become one of the most widely used bioinformatics tools for molecular biology research.Key features of BioEdit include:User-friendly graphical interface for editing and analyzing DNA, RNA, and protein sequencesSpecialized...
Geneious icon

Geneious

Geneious is a commercial bioinformatics software platform developed by Biomatters for DNA, RNA, and protein sequence analysis and manipulation. It provides an intuitive graphical user interface and integrates multiple commonly used tools for genomics research.Some key features of Geneious include:Sequence alignment with both global and local algorithmsPhylogenetic tree building tools...
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Vector NTI icon

Vector NTI

Vector NTI is a bioinformatics software package developed by Invitrogen for Windows, Mac, and Linux systems. It is used by molecular biologists, biochemists, and other life science researchers to manage, analyze, and visualize DNA, RNA, and protein sequencing data.Some key features of Vector NTI include:Sequence alignment tools for nucleotide and...
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Clustal Omega icon

Clustal Omega

Clustal Omega is a powerful multiple sequence alignment tool for aligning protein, DNA and RNA sequences. It is open-source and free to use. Clustal Omega uses advanced alignment algorithms like mBed and HHalign to enable the alignment of extremely large numbers (hundreds of thousands to millions) of sequences very quickly...
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CLC Main Workbench icon

CLC Main Workbench

CLC Main Workbench is a user-friendly desktop application that serves as an integrated environment for analyzing and visualizing next-generation sequencing (NGS) data across a wide range of applications. It provides robust tools for de novo assembly, mapping reads to a reference, analyzing variations, differential expression for RNA-Seq, metagenomic analysis, and...
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GeneDoc icon

GeneDoc

GeneDoc is a graphical tool designed for manipulating and editing genomic sequences. It enables users to efficiently view, edit, and annotate DNA or protein sequences up to 10Mb in length. Some of the key features of GeneDoc include:Six-frame translation - Automatically translate DNA sequences in all six reading framesORF finding...