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ORCIDAlgorithms for Molecular Biology, Volume 18
Volume 18, Number 1, December 2023
- Shaili Mathur, Noah A. Rosenberg
:
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees. 1 - Taher Mun, Naga Sai Kavya Vaddadi, Ben Langmead:
Pangenomic genotyping with the marker array. 2 - Giulio Ermanno Pibiri:
On weighted k-mer dictionaries. 3 - 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. 4 - Sebastian S. Schmidt, Jarno N. Alanko:
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time. 5 - Baqiao Liu, Tandy J. Warnow:
Weighted ASTRID: fast and accurate species trees from weighted internode distances. 6 - Ke Chen, Mingfu Shao:
Locality-sensitive bucketing functions for the edit distance. 7 - Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler:
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. 8 - Mathieu Gascon, Nadia El-Mabrouk:
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer. 9 - 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. 10 - Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, Lorenzo Tattini:
phyBWT2: phylogeny reconstruction via eBWT positional clustering. 11 - Yifan Jin, Jonathan Terhorst:
The solution surface of the Li-Stephens haplotype copying model. 12 - Giulia Bernardini, Leo van Iersel, Esther Julien, Leen Stougie:
Constructing phylogenetic networks via cherry picking and machine learning. 13 - Diego P. Rubert, Marília D. V. Braga:
Efficient gene orthology inference via large-scale rearrangements. 14 - Konstantinn Bonnet, Tobias Marschall, Daniel Doerr:
Constructing founder sets under allelic and non-allelic homologous recombination. 15 - David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Relative timing information and orthology in evolutionary scenarios. 16 - Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson:
New algorithms for structure informed genome rearrangement. 17 - Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty, Laurent Bulteau:
Automated design of dynamic programming schemes for RNA folding with pseudoknots. 18 - Yunheng Han, Erin K. Molloy:
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model. 19 - Konstantinn Bonnet, Tobias Marschall, Daniel Doerr:
Correction: Constructing founder sets under allelic and non-allelic homologous recombination. 20 - Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow:
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. 21
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