GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution [PDF]
BMC Genomics, 2018 Background Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the
Emmanuel Noutahi, Nadia El-Mabrouk
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An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model [PDF]
BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient
Santi Santichaivekin +2 more
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A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer [PDF]
, 2006 We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for
Miklós Csűrös, István Miklós
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The complete mitochondrial genome of Hyotissa sinensis (Bivalvia, Ostreoidea) indicates the genetic diversity within Gryphaeidae [PDF]
Biodiversity Data Journal, 2023 Different from the true oyster (family Ostreidae), the molecular diversity of the gryphaeid oyster (family Gryphaeidae) has never been sufficiently investigated.
Fengping Li +9 more
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Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages
Algorithms, 2021 Duplication-Transfer-Loss (DTL) reconciliation is a widely used computational technique for understanding gene family evolution and inferring horizontal gene transfer (transfer for short) in microbes.
Samson Weiner, Mukul S. Bansal
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xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
BMC Bioinformatics, 2023 To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation.
Nuo Liu +11 more
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The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. [PDF]
PLoS ONE, 2013 The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference
Daniel A Dalquen +3 more
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Maximum parsimony reconciliation in the DTLOR model
BMC Bioinformatics, 2021 Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of ...
Jingyi Liu +5 more
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Bacterial microevolution and the Pangenome [PDF]
, 2020 The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome.
A Bankevich +68 more
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Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. [PDF]
PLoS ONE, 2014 The sodium -pumping NADH: ubiquinone oxidoreductase (Na+-NQR) is the main ion pump and the primary entry site for electrons into the respiratory chain of many different types of pathogenic bacteria. This enzymatic complex creates a transmembrane gradient
Adrian Reyes-Prieto +2 more
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