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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

  12. 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
  13. 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
  14. 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
  15. Every tumor is composed of heterogeneous clones, each corresponding to a distinct subpopulation of cells that accumulated different types of somatic mutations, ranging from single-nucleotide variants (SNVs) to...

    Authors: Palash Sashittal, Simone Zaccaria and Mohammed El-Kebir
    Citation: Algorithms for Molecular Biology 2022 17:3
  16. Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length o...

    Authors: Tim Anderson and Travis J. Wheeler
    Citation: Algorithms for Molecular Biology 2021 16:25
  17. In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the gene...

    Authors: Klairton L. Brito, Andre R. Oliveira, Alexsandro O. Alexandrino, Ulisses Dias and Zanoni Dias
    Citation: Algorithms for Molecular Biology 2021 16:24
  18. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set L is known to be solvable i...

    Authors: David Schaller, Marc Hellmuth and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2021 16:23
  19. A semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose we are given a c...

    Authors: David Fernández-Baca and Lei Liu
    Citation: Algorithms for Molecular Biology 2021 16:22
  20. The rearrangement distance is a method to compare genomes of different species. Such distance is the number of rearrangement events necessary to transform one genome into another. Two commonly studied events a...

    Authors: Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira and Zanoni Dias
    Citation: Algorithms for Molecular Biology 2021 16:21
  21. Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...

    Authors: Fabian Hausmann and Stefan Kurtz
    Citation: Algorithms for Molecular Biology 2021 16:20
  22. Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics as a representation of the pairwise most closely related genes among multiple species. An arc connec...

    Authors: David Schaller, Manuela Geiß, Marc Hellmuth and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2021 16:19
  23. Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quant...

    Authors: Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi and Tatsuya Akutsu
    Citation: Algorithms for Molecular Biology 2021 16:18
  24. Prediction of drug resistance and identification of its mechanisms in bacteria such as Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a challenging problem. Solving this problem requires a ...

    Authors: Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht and Leonid Chindelevitch
    Citation: Algorithms for Molecular Biology 2021 16:17
  25. Gene clusters are groups of genes that are co-locally conserved across various genomes, not necessarily in the same order. Their discovery and analysis is valuable in tasks such as gene annotation and predicti...

    Authors: Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi and Michal Ziv-Ukelson
    Citation: Algorithms for Molecular Biology 2021 16:16
  26. In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous ti...

    Authors: Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin and Axel Mosig
    Citation: Algorithms for Molecular Biology 2021 16:15
  27. Directed evolution (DE) is a technique for protein engineering that involves iterative rounds of mutagenesis and screening to search for sequences that optimize a given property, such as binding affinity to a ...

    Authors: Trevor S. Frisby and Christopher James Langmead
    Citation: Algorithms for Molecular Biology 2021 16:13
  28. One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life i...

    Authors: Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2021 16:12
  29. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to ob...

    Authors: Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau
    Citation: Algorithms for Molecular Biology 2021 16:11
  30. K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a de...

    Authors: Amatur Rahman, Rayan Chikhi and Paul Medvedev
    Citation: Algorithms for Molecular Biology 2021 16:10
  31. Mutation trees are rooted trees in which nodes are of arbitrary degree and labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutati...

    Authors: Katharina Jahn, Niko Beerenwinkel and Louxin Zhang
    Citation: Algorithms for Molecular Biology 2021 16:9