Multiple Sequence Alignment

Benchmarks archive 2025-07-28

3 leaderboard tables shown for this task, 3 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

No dataset record in the archive lists this task.

Subtasks archive 2025-07-28

No subtask under this task in the archive's task tree.

Most implemented papers archive 2025-07-28

19 shown of 19 papers with code (54 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
  9 Nov 2019 3 repositories listed
  Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D…
• ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning
  1 Dec 2023 2 repositories listed
  Meanwhile, the ESM-NBR obtains the MCC values for DNA-binding residues prediction of 0.
• Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation
  2 Jun 2023 2 repositories listed
  The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision.
• Phylogenetic automata, pruning, and multiple alignment
  22 Mar 2011 2 repositories listed
  We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment.
• Expert-guided protein language models enable accurate and blazingly fast fitness prediction
  22 Nov 2024 1 repository listed
  Results To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from the human proteome applying the multiple sequence alignment-based effect predictor GEMME…
• MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
  8 Jun 2024 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families.
• PEvoLM: Protein Sequence Evolutionary Information Language Model
  16 Aug 2023 1 repository listed
  With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary…
• PoET: A generative model of protein families as sequences-of-sequences
  9 Jun 2023 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  Generative protein language models are a natural way to design new proteins with desired functions.
• Convolutional ProteinUnetLM competitive with long short-term memory-based protein secondary structure predictors
  30 Nov 2022 1 repository listed
  In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language models (pLMs) is emerging.
• ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
  20 Jul 2022 1 repository listed
  We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs.
• Exploring evolution-aware & -free protein language models as protein function predictors
  14 Jun 2022 1 repository listed Syntology ran 3 of 9 samples · 6 unverified
  Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions.
• Neural Distance Embeddings for Biological Sequences
  20 Sep 2021 1 repository listed Syntology ran 6 of 6 samples · 0 unverified
  The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research.
• MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences
  8 Jun 2021 1 repository listed
  We introduce MNHN-Tree-Tools, a high performance set of algorithms that builds multi-scale, nested clusters of sequences found in a FASTA file.
• MSA Transformer
  13 Feb 2021 1 repository listed
  Unsupervised protein language models trained across millions of diverse sequences learn structure and function of proteins.
• DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences
  21 Nov 2020 1 repository listed
  This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment method.
• Align-RUDDER: Learning From Few Demonstrations by Reward Redistribution
  29 Sep 2020 1 repository listed Syntology ran 0 of 3 samples · 3 unverified
  For such complex tasks, the recently proposed RUDDER uses reward redistribution to leverage steps in the Q-function that are associated with accomplishing sub-tasks.
• Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network
  30 Aug 2017 1 repository listed
  Nepal, the pairwise profile aligner with the novel scoring function significantly improved both alignment sensitivity and precision, compared to aligners with the existing functions.
• QuickProbs 2: towards rapid construction of high-quality alignments of large protein families
  30 Aug 2016 1 repository listed
  Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet.
• Ultra-large alignments using Phylogeny-aware Profiles
  5 Apr 2015 1 repository listed
  Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of…

Syntology lines on 5 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.