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- 1From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Recently one step mutation matrices were introduced to model the impact of substitutions on arbitrary branches of a phylogenetic tree on an alignment site. This concept works nicely for the four-state...
- 2From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for...
- 3From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedWe present optimal linear time algorithms for computing the Shapley values and 'heightened evolutionary distinctiveness' (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency of these...
- 4From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary...
- 5From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground We present a way to compute the minimal semi-positive invariants of a Petri net representing a biological reaction system, as resolution of a Constraint Satisfaction Problem. The use of Petri nets to...
- 6From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground First proposed by Cavender and Felsenstein, and Lake, invariant based algorithms for phylogenetic reconstruction were widely dismissed by practicing biologists because invariants were perceived to have...
- 7From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedA phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species...
- 8From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological...
- 9From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate...
- 10From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Traditional algorithms to solve the problem of sorting by signed reversals output just one optimal solution while the space of all optimal solutions can be huge. A so-called trace represents a group of...
- 11From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedAbstract Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences,...
- 12From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedMotivation Methods for simulating the kinetic folding of RNAs by numerically solving the chemical master equation have been developed since the late 90's, notably the programs Kinfold and Treekin with Barriers that...
- 13From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Through the wealth of information contained within them, genome-wide association studies (GWAS) have the potential to provide researchers with a systematic means of associating genetic variants with a wide...
- 14From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene...
- 15From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground In this paper, we study the problem of constructing perfect phylogenies for three-state characters. Our work builds on two recent results. The first result states that for three-state characters, the local...
- 16From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise...
- 17From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in "embedding" inferred gene trees into a known species tree, revealing the evolution of...
- 18From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the...
- 19From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root of phylogenetic trees, algorithmic methods to do so are lacking. Results In this paper we...
- 20From: Algorithms for Molecular Biology. (Vol. 7, Issue 1) Peer-ReviewedBackground The metagenomics approach allows the simultaneous sequencing of all genomes in an environmental sample. This results in high complexity datasets, where in addition to repeats and sequencing errors, the...