Volume 19; 2024

Research

Investigating the complexity of the double distance problems

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye

Algorithms Mol Biol. 2024; 19: 1. Published online 2024 Jan 4. doi: 10.1186/s13015-023-00246-y

PMCID:: PMC10765962

Article PDF–2.7M

Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem

Junyan Dai, Tobias Rubel, Yunheng Han, Erin K. Molloy

Algorithms Mol Biol. 2024; 19: 2. Published online 2024 Jan 8. doi: 10.1186/s13015-023-00249-9

PMCID:: PMC10775561

Article PDF–2.0M

Fulgor: a fast and compact k-mer index for large-scale matching and color queries

Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri, Rob Patro

Algorithms Mol Biol. 2024; 19: 3. Published online 2024 Jan 22. doi: 10.1186/s13015-024-00251-9

PMCID:: PMC10810250

Article PDF–2.3M

Predicting horizontal gene transfers with perfect transfer networks

Alitzel López Sánchez, Manuel Lafond

Algorithms Mol Biol. 2024; 19: 6. Published online 2024 Feb 6. doi: 10.1186/s13015-023-00242-2

PMCID:: PMC10848447

Article PDF–2.2M

Unifying duplication episode clustering and gene-species mapping inference

Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek

Algorithms Mol Biol. 2024; 19: 7. Published online 2024 Feb 14. doi: 10.1186/s13015-024-00252-8

PMCID:: PMC10865717

Article PDF–2.8M

Recombinations, chains and caps: resolving problems with the DCJ-indel model

Leonard Bohnenkämper

Algorithms Mol Biol. 2024; 19: 8. Published online 2024 Feb 27. doi: 10.1186/s13015-024-00253-7

PMCID:: PMC10900646

Article PDF–2.6M

Finding maximal exact matches in graphs

Nicola Rizzo, Manuel Cáceres, Veli Mäkinen

Algorithms Mol Biol. 2024; 19: 10. Published online 2024 Mar 11. doi: 10.1186/s13015-024-00255-5

PMCID:: PMC10929130

Article PDF–2.7M

Suffix sorting via matching statistics

Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi

Algorithms Mol Biol. 2024; 19: 11. Published online 2024 Mar 12. doi: 10.1186/s13015-023-00245-z

PMCID:: PMC10935992

Article PDF–2.5M

Median quartet tree search algorithms using optimal subtree prune and regraft

Shayesteh Arasti, Siavash Mirarab

Algorithms Mol Biol. 2024; 19: 12. Published online 2024 Mar 13. doi: 10.1186/s13015-024-00257-3

PMCID:: PMC10938725

Article PDF–3.1M

Infrared: a declarative tree decomposition-powered framework for bioinformatics

Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will

Algorithms Mol Biol. 2024; 19: 13. Published online 2024 Mar 16. doi: 10.1186/s13015-024-00258-2

PMCID:: PMC10943887

Article PDF–3.6M

Space-efficient computation of k-mer dictionaries for large values of k

Diego Díaz-Domínguez, Miika Leinonen, Leena Salmela

Algorithms Mol Biol. 2024; 19: 14. Published online 2024 Apr 5. doi: 10.1186/s13015-024-00259-1

PMCID:: PMC10996146

Article PDF–3.6M

Pfp-fm: an accelerated FM-index

Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie

Algorithms Mol Biol. 2024; 19: 15. Published online 2024 Apr 10. doi: 10.1186/s13015-024-00260-8

PMCID:: PMC11005213

Article PDF–2.7M

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