Related papers: SICLE: A high-throughput tool for extracting evolu…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Malware lineage studies the evolutionary relationships among malware and has important applications for malware analysis. A persistent limitation of prior malware lineage approaches is to consider every input sample a separate malware…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are…
Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the…
CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequence…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
The Saliency Model Implementation Library for Experimental Research (SMILER) is a new software package which provides an open, standardized, and extensible framework for maintaining and executing computational saliency models. This work…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
We introduce a technique to filter out complex data-sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…