The Small Parsimony Problem (SPP) aims at finding the gene orders at internal nodes of a given phylogenetic tree such that the overall genome rearrangement distance along the tree branches is minimized. This problem is intractable in most genome rearrangement models, especially when gene duplication and loss are considered. In this work, we describe an Integer Linear Program algorithm to solve the SPP for natural genomes, i.e. genomes that contain conserved, unique, and duplicated markers. The evolutionary model that we consider is the DCJ-indel model that includes the Double-Cut and Join rearrangement operation and the insertion and deletion of genome segments. We evaluate our algorithm on simulated data and show that it is able to reconstruct very efficiently and accurately ancestral gene orders in a very comprehensive evolutionary model.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1142/S0219720021400096 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Training and validating a treatment recommender with partial verification evidence.
Artif Intell Med
December 2024
Knowledge Management & Discovery Lab, Otto-von-Guericke-University Magdeburg, Germany. Electronic address:
Background: Current clinical decision support systems (DSS) are trained and validated on observational data from the clinic in which the DSS is going to be applied. This is problematic for treatments that have already been validated in a randomized clinical trial (RCT), but have not yet been introduced in any clinic. In this work, we report on a method for training and validating the DSS core before introduction to a clinic, using the RCT data themselves.
View Article and Find Full Text PDFMinLinMo: a minimalist approach to variable selection and linear model prediction.
BMC Bioinformatics
December 2024
Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
Generating prediction models from high dimensional data often result in large models with many predictors. Causal inference for such models can therefore be difficult or even impossible in practice. The stand-alone software package MinLinMo emphasizes small linear prediction models over highest possible predictability with a particular focus on including variables correlated with the outcome, minimal memory usage and speed.
View Article and Find Full Text PDFDevonian Harpetidae from the central and eastern Anti-Atlas, Morocco.
Zootaxa
May 2024
12 Crescent Grove; London SW4 7AH; UK.
The systematics of 37 new species of Devonian Harpetidae from the central and eastern Anti-Atlas Mountains, Morocco, are described. The new material comes from the Dra-Tafilalet region and the province of Tata. A cladistic study was undertaken involving 138 taxa with the objective of assigning the new taxa to the appropriate genera, which are, as far as possible, monophyletic.
View Article and Find Full Text PDFBayesian factor selection in a hybrid approach to confirmatory factor analysis.
J Appl Stat
April 2024
Department of Biostatistics, University at Buffalo, State University of New York, Buffalo, NY, USA.
To investigate latent structures of measured variables, various factor structures are used for confirmatory factor analysis, including higher-order models and more flexible bifactor models. In practice, measured variables may also have relatively small or moderate non-zero loadings on multiple group factors, which form cross loadings. The selection of correct and 'identifiable' latent structures is important to evaluate an impact of constructs of interest in the confirmatory factor analysis model.
View Article and Find Full Text PDFNever ending diversity: two new species of the genus (Digenea: Allocreadiidae) including new keys to the genus.
J Helminthol
October 2024
A. V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690041, 17 Palchevskogo Street, Russian Federation.
Two new species of the genus were isolated from the intestines of the Lake minnow caught in the backwater of the Komissarovka River in the South of the Russian Far East. The morphology of n. sp.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!