发表论文

MSA

1. HAlign 3: fast multiple alignment of ultra-large numbers of similar DNA/RNA sequences. Molecular Biology and Evolution. 2022 (soft)

2. HAlign 4: a new strategy for rapidly aligning millions of sequences. Bioinformatics. 2024 (soft)

数据集推荐:适合处理序列数量极多、长度中等、整体相似度较高的数据集。

3. FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. Bioinformatics. 2024 (soft)

数据集推荐:适合序列数量少，但单条序列长度很长，且整体相似度较高的数据集。

4. minipoa: A minimizer-based method for fast and memory-efficient partial order alignment. biorixv. 2026 (soft)

数据集推荐:适合序列数量中等，序列长度长，且整体相似度在中等以上的数据集。

MSA post-processing

1. TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. PLOS COMPUTATIONAL BIOLOGY. 2024 (soft)

2. ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments. NAR Genomics and Bioinformatics. 2024 (soft)

3. ReAlign-Star: an optimized realignment method for multiple sequence alignment, targeting star algorithm tools. International Conference on Intelligent Computing. 2025 (soft)

4. ReAlign-P: a vertical iterative realignment method for protein multiple sequence alignment. Bioinformatics. 2025 (soft)

MGA

1. Fast sequence alignment for centromere with RaMA. Genome Research. 2025 (soft)

2. HAlign-G : rapid and low-memory multiple-genome aligner for large-scale closely related genomes. Genome Biology. 2025 (soft)

PSA

1. FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity. Briefings in Bioinformatics. 2025 (soft)

Review

1. Developments in Algorithms for Sequence Alignment: A Review. Biomolecules. 2022

2. A survey on the algorithm and development of multiple sequence alignment. Briefings in Bioinformatics. 2022

3. Advances in post-processing methods for multiple sequence alignment. Frontiers in Genetics. 2025

其他论文

1. HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy. Bioinformatics. 2015 (soft)

2. HAlign 2: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing. Algorithms for Molecular Biology. 2017 (soft)

3. FMAlign: A novel fast multiple nucleotide sequence alignment method based on FM-index. Briefings in Bioinformatics. 2021

4. CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment. BMC Bioinformatics. 2017 (soft)

5. Reconstructing evolutionary trees in parallel for massive sequences. BMC Systems Biology. 2017

6. Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework. Journal of Computational Biology. 2017 (soft)

7. VCSRA: A fast and accurate multiple sequence alignment algorithm with a high degree of parallelism. Journal of Genetics and Genomics. 2018 (soft)

8. Improved Center Star Alignment Algorithm Based on Profile Alignment. Journal of University of Electronic Science and Technology of China. 2022

9. WMSA: a novel method for multiple sequence alignment of DNA sequences. Bioinformatics. 2022 (soft)

10. WMSA2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies. Briefings in Bioinformatics. 2023 (soft)

11. deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment. GigaScience. 2026 (soft)