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Algorithms Mol. Biol.
2006
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2018
2024
2006
2024
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Publications
volume 19, number 1, 2024
Junyan Dai
,
Tobias Rubel
,
Yunheng Han
,
Erin K. Molloy
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.
Algorithms Mol. Biol.
19 (1) (2024)
Alitzel López Sánchez
,
Manuel Lafond
Predicting horizontal gene transfers with perfect transfer networks.
Algorithms Mol. Biol.
19 (1) (2024)
Pawel Górecki
,
Natalia Rutecka
,
Agnieszka Mykowiecka
,
Jaroslaw Paszek
Unifying duplication episode clustering and gene-species mapping inference.
Algorithms Mol. Biol.
19 (1) (2024)
Victor Epain
,
Rumen Andonov
Global exact optimisations for chloroplast structural haplotype scaffolding.
Algorithms Mol. Biol.
19 (1) (2024)
Jyotshna Rajput
,
Ghanshyam Chandra
,
Chirag Jain
Co-linear chaining on pangenome graphs.
Algorithms Mol. Biol.
19 (1) (2024)
Jason Fan
,
Jamshed Khan
,
Noor Pratap Singh
,
Giulio Ermanno Pibiri
,
Rob Patro
Fulgor: a fast and compact k-mer index for large-scale matching and color queries.
Algorithms Mol. Biol.
19 (1) (2024)
Marília D. V. Braga
,
Leonie R. Brockmann
,
Katharina Klerx
,
Jens Stoye
Investigating the complexity of the double distance problems.
Algorithms Mol. Biol.
19 (1) (2024)
volume 18, number 1, 2023
Veronica Guerrini
,
Alessio Conte
,
Roberto Grossi
,
Gianni Liti
,
Giovanna Rosone
,
Lorenzo Tattini
phyBWT2: phylogeny reconstruction via eBWT positional clustering.
Algorithms Mol. Biol.
18 (1) (2023)
Taher Mun
,
Vaddadi Naga Sai Kavya
,
Ben Langmead
Pangenomic genotyping with the marker array.
Algorithms Mol. Biol.
18 (1) (2023)
Yifan Jin
,
Jonathan Terhorst
The solution surface of the Li-Stephens haplotype copying model.
Algorithms Mol. Biol.
18 (1) (2023)
Eden Ozeri
,
Meirav Zehavi
,
Michal Ziv-Ukelson
New algorithms for structure informed genome rearrangement.
Algorithms Mol. Biol.
18 (1) (2023)
Diego P. Rubert
,
Marília D. V. Braga
Efficient gene orthology inference via large-scale rearrangements.
Algorithms Mol. Biol.
18 (1) (2023)
Sebastian S. Schmidt
,
Jarno N. Alanko
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.
Algorithms Mol. Biol.
18 (1) (2023)
Seong-Hwan Jun
,
Hassan Nasif
,
Chris Jennings-Shaffer
,
David H. Rich
,
Anna Kooperberg
,
Mathieu Fourment
,
Cheng Zhang
,
Marc A. Suchard
,
Frederick A. Matsen IV
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.
Algorithms Mol. Biol.
18 (1) (2023)
Ke Chen
,
Mingfu Shao
Locality-sensitive bucketing functions for the edit distance.
Algorithms Mol. Biol.
18 (1) (2023)
Shaili Mathur
,
Noah A. Rosenberg
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees.
Algorithms Mol. Biol.
18 (1) (2023)
Konstantinn Bonnet
,
Tobias Marschall
,
Daniel Doerr
Correction: Constructing founder sets under allelic and non-allelic homologous recombination.
Algorithms Mol. Biol.
18 (1) (2023)
Hua-Ting Yao
,
Ronny Lorenz
,
Ivo L. Hofacker
,
Peter F. Stadler
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.
Algorithms Mol. Biol.
18 (1) (2023)
Mathieu Gascon
,
Nadia El-Mabrouk
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer.
Algorithms Mol. Biol.
18 (1) (2023)
Yunheng Han
,
Erin K. Molloy
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model.
Algorithms Mol. Biol.
18 (1) (2023)
Bertrand Marchand
,
Sebastian Will
,
Sarah J. Berkemer
,
Yann Ponty
,
Laurent Bulteau
Automated design of dynamic programming schemes for RNA folding with pseudoknots.
Algorithms Mol. Biol.
18 (1) (2023)
Giulio Ermanno Pibiri
On weighted k-mer dictionaries.
Algorithms Mol. Biol.
18 (1) (2023)
Chengze Shen
,
Baqiao Liu
,
Kelly P. Williams
,
Tandy J. Warnow
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment.
Algorithms Mol. Biol.
18 (1) (2023)
David Schaller
,
Tom Hartmann
,
Manuel Lafond
,
Peter F. Stadler
,
Nicolas Wieseke
,
Marc Hellmuth
Relative timing information and orthology in evolutionary scenarios.
Algorithms Mol. Biol.
18 (1) (2023)
Baqiao Liu
,
Tandy J. Warnow
Weighted ASTRID: fast and accurate species trees from weighted internode distances.
Algorithms Mol. Biol.
18 (1) (2023)
Konstantinn Bonnet
,
Tobias Marschall
,
Daniel Doerr
Constructing founder sets under allelic and non-allelic homologous recombination.
Algorithms Mol. Biol.
18 (1) (2023)
Giulia Bernardini
,
Leo van Iersel
,
Esther Julien
,
Leen Stougie
Constructing phylogenetic networks via cherry picking and machine learning.
Algorithms Mol. Biol.
18 (1) (2023)
Mohammad Fili
,
Guiping Hu
,
Changze Han
,
Alexa Kort
,
John Trettin
,
Hillel Haim
A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients.
Algorithms Mol. Biol.
18 (1) (2023)
volume 17, number 1, 2022
Marcin Wawerka
,
Dawid Dabkowski
,
Natalia Rutecka
,
Agnieszka Mykowiecka
,
Pawel Górecki
Embedding gene trees into phylogenetic networks by conflict resolution algorithms.
Algorithms Mol. Biol.
17 (1) (2022)
Yishu Wang
,
Arnaud Mary
,
Marie-France Sagot
,
Blerina Sinaimeri
Efficiently sparse listing of classes of optimal cophylogeny reconciliations.
Algorithms Mol. Biol.
17 (1) (2022)
Peter F. Stadler
,
Sebastian Will
Bi-alignments with affine gaps costs.
Algorithms Mol. Biol.
17 (1) (2022)
Palash Sashittal
,
Simone Zaccaria
,
Mohammed El-Kebir
Parsimonious Clone Tree Integration in cancer.
Algorithms Mol. Biol.
17 (1) (2022)
Spencer Krieger
,
John D. Kececioglu
Heuristic shortest hyperpaths in cell signaling hypergraphs.
Algorithms Mol. Biol.
17 (1) (2022)
Yue Wang
Two metrics on rooted unordered trees with labels.
Algorithms Mol. Biol.
17 (1) (2022)
Luiz Augusto G. Silva
,
Luis Antonio B. Kowada
,
Noraí Romeu Rocco
,
Maria Emília M. T. Walter
A new 1.375-approximation algorithm for sorting by transpositions.
Algorithms Mol. Biol.
17 (1) (2022)
Spencer Krieger
,
John D. Kececioglu
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs.
Algorithms Mol. Biol.
17 (1) (2022)
Anuradha Wickramarachchi
,
Yu Lin
Binning long reads in metagenomics datasets using composition and coverage information.
Algorithms Mol. Biol.
17 (1) (2022)
Yoshiki Nakagawa
,
Satsuya Ohata
,
Kana Shimizu
Efficient privacy-preserving variable-length substring match for genome sequence.
Algorithms Mol. Biol.
17 (1) (2022)
Jason Fan
,
Skylar Chan
,
Rob Patro
Perplexity: evaluating transcript abundance estimation in the absence of ground truth.
Algorithms Mol. Biol.
17 (1) (2022)
Yoshihiro Shibuya
,
Djamal Belazzougui
,
Gregory Kucherov
Space-efficient representation of genomic k-mer count tables.
Algorithms Mol. Biol.
17 (1) (2022)
Tom Davot
,
Annie Chateau
,
Rohan Fossé
,
Rodolphe Giroudeau
,
Mathias Weller
On a greedy approach for genome scaffolding.
Algorithms Mol. Biol.
17 (1) (2022)
Bertrand Marchand
,
Yann Ponty
,
Laurent Bulteau
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics.
Algorithms Mol. Biol.
17 (1) (2022)
Hamza Iseric
,
Can Alkan
,
Faraz Hach
,
Ibrahim Numanagic
Fast characterization of segmental duplication structure in multiple genome assemblies.
Algorithms Mol. Biol.
17 (1) (2022)
Céline Scornavacca
,
Mathias Weller
Treewidth-based algorithms for the small parsimony problem on networks.
Algorithms Mol. Biol.
17 (1) (2022)
Patrick Kunzmann
,
Jacob Marcel Anter
,
Kay Hamacher
Adding hydrogen atoms to molecular models via fragment superimposition.
Algorithms Mol. Biol.
17 (1) (2022)
volume 16, number 1, 2021
Amatur Rahman
,
Rayan Chikhi
,
Paul Medvedev
Disk compression of k-mer sets.
Algorithms Mol. Biol.
16 (1) (2021)
Klairton Lima Brito
,
Andre Rodrigues Oliveira
,
Alexsandro Oliveira Alexandrino
,
Ulisses Dias
,
Zanoni Dias
An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes.
Algorithms Mol. Biol.
16 (1) (2021)
Katharina Jahn
,
Niko Beerenwinkel
,
Louxin Zhang
The Bourque distances for mutation trees of cancers.
Algorithms Mol. Biol.
16 (1) (2021)
Trevor S. Frisby
,
Christopher James Langmead
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution.
Algorithms Mol. Biol.
16 (1) (2021)
Thomas Gatter
,
Sarah von Löhneysen
,
Jörg Fallmann
,
Polina Drozdova
,
Tom Hartmann
,
Peter F. Stadler
LazyB: fast and cheap genome assembly.
Algorithms Mol. Biol.
16 (1) (2021)