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MaxAlign 1.1 Server

A tool to remove sequences (taxa) with many gaps in the post-process of alignments in order to improve the alignment area

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic analyses, for instance, gapped columns are often discarded entirely from the alignment.
MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of characters that are present in gap-free columns - alignment area - by selecting an optimal subset of sequences. MaxAlign can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.

Instructions Output format Algorithm description Article abstract


Paste your alignment in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

At most 3000 sequences per submission; maximal sequence length of 5,000 residues.

The sequences are kept confidential and will be deleted after processing.


Delete columns in result if only gaps in column
Detailed output
Ensure optimal solution (costly)

If you want to use a protein alignment but obtain the output in nucleotides, please submit the nucleotide alignment below (you must still submit the protein alignment in the field on the top of the page).
The fasta identifiers for every sequence must be identical in the two alignments.

Submit a second fasta file in FASTA format directly from your local disk:


For publication of results, please cite:

MaxAlign: maximizing usable data in an alignment
BMC Bioinformatics 2007, 8:312
Gouveia-Oliveira R, Sackett P W, Pedersen A G

View the abstract.
View the supplementary material.

Downloadable Version

Would you prefer to run MaxAlign at your own machine?
MaxAlign 1.1 is available for download. Right-click - Save as.
You need a perl installation to run MaxAlign, but nothing else as the program is made in pure perl and requires no extra modules.

Web Service Version

MaxAlign is also available as a Web Service here:


Scientific problems:        Technical problems: