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Abalign is a comprehensive multiple sequence alignment(MSA) software for B-cell receptor immune repertoires, offering an ultrafast MSA capability and a wide range of analytical features, including BCR/Antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization and more. Importantly, users can perform these analyses using the graphical user interface without requiring any programming skills or scripts. Abalign can be easily run on personal computers equipped with Linux, Mac, or Windows operating systems, delivering significant advantages in speed, accuracy, and memory consumption.

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F Zong, C Long, W Hu, S Chen, W Dai, ZX Xiao, Y Cao* . Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Research. 2023.

Abalign is a comprehensive platform for BCR immune repertoires analysis
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Fig 1. The working pipeline of Abalign.

Based on its state-of-the-art performance in MSA, Abalign provides antibody numbering, CDRs and FRs recognition, VJ gene identifying, B-cell Lineage tree constructing, clonotype analysis, residue preference, diversity analysis, etc. Beyond that, Abalign supports multi-file cross-analysis, which is super convenient for BCR immune repertoires.

Abalign is a state-of-the-art MSA method.
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Fig 1. The result of IS and CS scores of MSAs.

We compared Abalign with three state-of-the-art MSA tools: Clustal Omega, MAFFT, MUSLCE in terms of accuracy, usability, time and memory consumption. The average scores of the four tools for three samples are shown in the figure. In terms of SP and TC scores, Abalign outperformed the other three tools, indicating that the multiple sequence alignment results of Abalign substantially improved the MSA for BCR or antibody sequences.