Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Davín, Adrián; Tricou, Théo; Tannier, Éric; Vienne, Damien M. de; Szöllősi, Gergely J

doi:10.1101/339473

Cited by 4 publications

(3 citation statements)

References 24 publications

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“…We ran experiments on simulated data in order to evaluate the ability of the ILP to correctly predict the gene order of the median genome. The input for the program, including gene orders for the ancestor genome A and the descendant genomes D i , along with the orthology relations, generated using the ZOMBI genome simulator [8]. The ILP was solved using the Gurobi solver.…”

Section: Resultsmentioning

confidence: 99%

The Rooted SCJ Median with Single Gene Duplications

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Feijão

et al. 2018

Comparative Genomics

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The median problem is a classical problem in genome rearrangements. It aims to compute a gene order that minimizes the sum of the genomic distances to k ≥ 3 given gene orders. This problem is intractable except in the related Single-Cut-or-Join and breakpoint rearrangement models. Here we consider the rooted median problem, where we assume one of the given genomes to be ancestral to the median, which is itself ancestral to the other genomes. We show that in the Single-Cutor-Join model with single gene duplications, the rooted median problem is NP-hard. We also describe an Integer Linear Program for solving this problem, which we apply to simulated data, showing high accuracy of the reconstructed medians.

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Section: Resultsmentioning

confidence: 99%

The Rooted SCJ Median with Single Gene Duplications

Mane

Lafond

Feijão

et al. 2018

Comparative Genomics

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“…This will be based on simulations of genome evolution under a similar DTL model that accounts for gene linkage evolution. Simulation could be provided by pangenome tree simulators such as FwdTreeSim (https://github.com/flass/FwdTreeSim) or Zombi (Davin et al 2018). Development of analytical solutions to evaluate the likelihood of observing co-evolving pairs under a neutral model is also envisaged, notably using a linear algebra framework (Behdenna et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel

Lassalle

Veber

Jauneikaite

et al. 2019

Preprint

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The availability of bacterial pangenome data grows exponentially, requiring efficient new methods of analysis. Currently popular approaches for the fast comparison of genomes have the drawback of not being based on explicit evolutionary models of diversification. Making sense of bacterial genome evolution, and notably in the accessory genome, requires however to take into account the complex processes by which the genomes evolve. Here we present the Pantagruel bioinformatic software pipeline, which enables the construction of a complete bacterial pangenome database geared towards the inference of gene evolution scenarios using gene tree/species tree reconciliation. Pantagruel is a modular pipeline that combines state-of-the-art external software with unique new methods. It can be executed with no supervision to perform a standard pangenome analysis, or be configured by advanced users to integrate methods of choice. A relational database underlies its data structure, allowing efficient retrieval of the large-scale data generated by integrative analyses of pangenome evolutionary history. From the reconstructed gene evolution scenarios, two main outputs are derived: firstly the gene tree-aware assignation of orthology, allowing the fine analysis of gene gain and loss history over the species phylogeny, and secondly a network of gene-to-gene association based on correlated events in scenarios of gene evolution, leading to the definition of co-evolved gene modules. Pantagruel is available as an open source software package at https://github.com/flass/pantagruel.

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“…Next, we ran experiments on simulated data in order to evaluate the ability of the ILP to correctly predict the gene order of the median genome. The input for the program, including gene orders for the ancestor genome A and the descendant genomes D i , along with the orthology relations, generated using the ZOMBI genome simulator [27]. The ILP was solved using the Gurobi solver.…”

Section: The Rooted Median Problemmentioning

confidence: 99%

The distance and median problems in the single-cut-or-join model with single-gene duplications

Mane

Lafond

Feijão

et al. 2020

Algorithms Mol Biol

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Background. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. Results. We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Conclusion. Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances.

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Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Cited by 4 publications

References 24 publications

The Rooted SCJ Median with Single Gene Duplications

The Rooted SCJ Median with Single Gene Duplications

Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel

The distance and median problems in the single-cut-or-join model with single-gene duplications

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