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Abalign is a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.

High-throughput sequencing of B-cell immune repertoires has transformed our understanding of the adaptive immune response to various diseases. However, processing the vast amount of data generated by these technologies remains a significant challenge. We introduce Abalign, a novel high-throughput multiple sequence alignment (MSA) software specifically designed for aligning B-cell receptor (BCR) sequences. Benchmark tests demonstrate that Abalign outperforms existing MSA tools, delivering significant advantages in speed, accuracy, and memory consumption, reducing the time required for large-scale analysis from weeks to hours.

Abalign is a comprehensive platform for analyzing BCR immune repertoires, offering an ultrafast MSA capability and seamless integration with a wide range of analytical features, including BCR extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, 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, making it accessible to a wide range of users.

In summary, Abalign represents a powerful and user-friendly tool for analyzing BCR sequencing data, addressing a crucial need for researchers in the field of immunology.

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.

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.


Zong, F., Long, C., Hu, W. et al. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. In preparation.