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The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and wide...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have con...

"This work describes the use of entomological studies combined with in silico models (computer simulations derived from numerical models) to assess the efficacy of a novel device for controlled release of spatial repel...

Globally optimal triangulations are difficult to be found by deterministic methods as, for most type of criteria, no polynomial algorithm is known. In this work, we consider the Minimum Weight Triangulation (MWT) problem...

The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crysta...

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we intro...

The resolution of optimization problems is of great interest nowadays and has encouraged the development of various information technology methods to attempt solving them. There are several problems related to Software E...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains ...

BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, i...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, an...

ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40-60-fold faster search and optimized model utiliz...

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of spec...

(NOTE: Each chapter begins with an Introduction, and concludes with Exercises and References.) I. GETTING STARTED. 1. Aspects of Multivariate Analysis. Applications of Multivariate Techniques. The Organization of Data. D...

Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1–4 , the structures of around 100,000 un...