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.
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.
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: