9 papers · ranked by Valyu relevance
Carmel Farage, Daniel Edler, Anna Eklöf, Martin Rosvall + 1 more
Ecological networks often have a modular structure with groups of nodes that interact strongly within the group and weakly with other nodes in the network. A modular structure can reveal underlying dynamic ecological or evolutionary processes, influence dynamics that operate on the network, and affect network…
Svenn-Arne Dragly, Milad Hobbi Mobarhan, Mikkel Lepperød, Simen Tennøe + 3 more
Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available…
Lucas Czech, Jaime Huerta-Cepas, Alexandros Stamatakis
Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Virtually all empirical evolutionary data studies contain a visualization of the inferred tree with branch support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations…
Bradly Alicea, Thomas E. Portegys, Richard Gordon
Lineage trees of embryonic development contain much subtle information about the embryogenetic process. One type of information is contained in how the order of nodes are sorted at each level of the tree. Sorting of lineage trees is accomplished using a specific criterion for all levels (each representing a division…
William H. Piel, Rutger A. Vos
Over the last 20 years, TreeBASE has acquired a substantial body of phylogenetic data, including more than 20,000 published phylogenies. Given latency issues and limited options when it comes to querying the database remotely, a simplified and consolidated version of the database, here called TreeBASEdmp, is made…
Noam Teyssier, Alexander Dobin
Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput processing due to its reliance on single-threaded decompression and sequential parsing of irregularly sized records. This…
Hadi Poormohammadi, Mohsen Sardari Zarchi
Phylogenetic networks construction is one the most important challenge in phylogenetics. These networks can present complex non-treelike events such as gene flow, horizontal gene transfers, recombination or hybridizations. Among phylogenetic networks, rooted structures are commonly used to represent the evolutionary…
Lijia Jia, Yue Shi, Jing Yang, Shangzhe Li + 14 more
The explosive growth of digital data is overwhelming conventional storage media, creating an urgent need for more efficient solutions. DNA offers immense potential for digital data storage, yet most systems remain static and archival. Here, we present a modular DNA storage architecture based on dynamic DNA bytes…
Heng Li, Jiazhen Rong
We present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk employs implicit interval tree, a new data structure for fast interval overlap queries. It is several to tens of times…