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  1. FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-b...

    Authors: Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher and Travis Gagie
    Citation: Algorithms for Molecular Biology 2024 19:15
  2. Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailore...

    Authors: Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty and Sebastian Will
    Citation: Algorithms for Molecular Biology 2024 19:13
  3. We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the...

    Authors: Zsuzsanna Lipták, Francesco Masillo and Simon J. Puglisi
    Citation: Algorithms for Molecular Biology 2024 19:11
  4. We study the problem of finding maximal exact matches (MEMs) between a query string Q and a labeled graph G. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment metho...

    Authors: Nicola Rizzo, Manuel Cáceres and Veli Mäkinen
    Citation: Algorithms for Molecular Biology 2024 19:10
  5. We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC)...

    Authors: Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka and Jarosław Paszek
    Citation: Algorithms for Molecular Biology 2024 19:7
  6. Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to t...

    Authors: Jyotshna Rajput, Ghanshyam Chandra and Chirag Jain
    Citation: Algorithms for Molecular Biology 2024 19:4
  7. The problem of sequence identification or matching—determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence—is relevant for many imp...

    Authors: Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri and Rob Patro
    Citation: Algorithms for Molecular Biology 2024 19:3
  8. The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal wi...

    Authors: Junyan Dai, Tobias Rubel, Yunheng Han and Erin K. Molloy
    Citation: Algorithms for Molecular Biology 2024 19:2
  9. Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed usin...

    Authors: Chengze Shen, Baqiao Liu, Kelly P. Williams and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2023 18:21
  10. Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. Although many methods exist to estimate evolutionary trees (called phylogenies) from molecular sequ...

    Authors: Yunheng Han and Erin K. Molloy
    Citation: Algorithms for Molecular Biology 2023 18:19
  11. Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since t...

    Authors: Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty and Laurent Bulteau
    Citation: Algorithms for Molecular Biology 2023 18:18
  12. We define two new computational problems in the domain of perfect genome rearrangements, and propose three algorithms to solve them. The rearrangement scenarios modeled by the problems consider Reversal and Bl...

    Authors: Eden Ozeri, Meirav Zehavi and Michal Ziv-Ukelson
    Citation: Algorithms for Molecular Biology 2023 18:17
  13. Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative ti...

    Authors: David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke and Marc Hellmuth
    Citation: Algorithms for Molecular Biology 2023 18:16
  14. Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism ...

    Authors: Konstantinn Bonnet, Tobias Marschall and Daniel Doerr
    Citation: Algorithms for Molecular Biology 2023 18:15

    The Correction to this article has been published in Algorithms for Molecular Biology 2023 18:20

  15. Recently we developed a gene orthology inference tool based on genome rearrangements (Journal of Bioinformatics and Computational Biology 19:6, 2021). Given a set of genomes our method first computes all pairwise...

    Authors: Diego P. Rubert and Marília D. V. Braga
    Citation: Algorithms for Molecular Biology 2023 18:14
  16. The Li-Stephens (LS) haplotype copying model forms the basis of a number of important statistical inference procedures in genetics. LS is a probabilistic generative model which supposes that a sampled chromoso...

    Authors: Yifan Jin and Jonathan Terhorst
    Citation: Algorithms for Molecular Biology 2023 18:12
  17. Molecular phylogenetics studies the evolutionary relationships among the individuals of a population through their biological sequences. It may provide insights about the origin and the evolution of viral dise...

    Authors: Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone and Lorenzo Tattini
    Citation: Algorithms for Molecular Biology 2023 18:11
  18. Bayesian phylogenetics is a computationally challenging inferential problem. Classical methods are based on random-walk Markov chain Monte Carlo (MCMC), where random proposals are made on the tree parameter an...

    Authors: Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A Suchard and Frederick A Matsen IV
    Citation: Algorithms for Molecular Biology 2023 18:10
  19. Many bioinformatics applications involve bucketing a set of sequences where each sequence is allowed to be assigned into multiple buckets. To achieve both high sensitivity and precision, bucketing methods are ...

    Authors: Ke Chen and Mingfu Shao
    Citation: Algorithms for Molecular Biology 2023 18:7
  20. Therapeutics against the envelope (Env) proteins of human immunodeficiency virus type 1 (HIV-1) effectively reduce viral loads in patients. However, due to mutations, new therapy-resistant Env variants frequen...

    Authors: Mohammad Fili, Guiping Hu, Changze Han, Alexa Kort, John Trettin and Hillel Haim
    Citation: Algorithms for Molecular Biology 2023 18:4
  21. We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the...

    Authors: Taher Mun, Naga Sai Kavya Vaddadi and Ben Langmead
    Citation: Algorithms for Molecular Biology 2023 18:2
  22. Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem...

    Authors: Tom Davot, Annie Chateau, Rohan Fossé, Rodolphe Giroudeau and Mathias Weller
    Citation: Algorithms for Molecular Biology 2022 17:16
  23. The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a d...

    Authors: Yue Wang
    Citation: Algorithms for Molecular Biology 2022 17:13
  24. Cell signaling pathways, which are a series of reactions that start at receptors and end at transcription factors, are basic to systems biology. Properly modeling the reactions in such pathways requires directed ...

    Authors: Spencer Krieger and John Kececioglu
    Citation: Algorithms for Molecular Biology 2022 17:12

    The Correction to this article has been published in Algorithms for Molecular Biology 2022 17:17

  25. Phylogenetic networks are mathematical models of evolutionary processes involving reticulate events such as hybridization, recombination, or horizontal gene transfer. One of the crucial notions in phylogenetic...

    Authors: Marcin Wawerka, Dawid Dąbkowski, Natalia Rutecka, Agnieszka Mykowiecka and Paweł Górecki
    Citation: Algorithms for Molecular Biology 2022 17:11
  26. Commonly, sequence and structure elements are assumed to evolve congruently, such that homologous sequence positions correspond to homologous structural features. Assuming congruent evolution, alignments based on...

    Authors: Peter F. Stadler and Sebastian Will
    Citation: Algorithms for Molecular Biology 2022 17:10
  27. k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k-mers and counts, easily reaching tens of...

    Authors: Yoshihiro Shibuya, Djamal Belazzougui and Gregory Kucherov
    Citation: Algorithms for Molecular Biology 2022 17:5