相关论文: A format for phylogenetic placements

An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…

This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents…

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…

LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…

This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents…

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…

The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…

Semi-structured data formats such as JSON have proved to be useful data models for applications that require flexibility in the format of data stored. However, JSON data often come without the schemas that are typically available with…

Large, open datasets can accelerate ecological research, particularly by enabling researchers to develop new insights by reusing datasets from multiple sources. However, to find the most suitable datasets to combine and integrate,…

The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…

The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…

The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…

JSON (JavaScript Object Notation) is a data encoding that allows structured data to be used in a standardized and straightforward manner across systems. Schemas for JSON-formatted data can be constructed using the JSON Schema standard,…

To use heterogeneous hardware, programmers must have sufficient technical skills to utilize OpenMP, CUDA, and OpenCL. On the basis of this, I have proposed environment-adaptive software that enables automatic conversion, configuration, and…

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…