The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination.
Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Aims to construct and draw phylogenetic trees. TREECON offers functions to compute the evolutionary distance for all pairs of organisms or sequences. It infers a phylogenetic tree by considering the relationship between the distance values. This tool includes different types of programs for several functions: to root the unrooted evolutionary trees; to draw the tree on the screen; and to save the tree.
Builds phylogenetic networks for evolutionary analyzing. NeighborNet is an algorithm offering a distance-based method derived from the Neighbor-Joining approach. It exploits similar selection and reduction formulae and is consistent for all circular distance matrices. The algorithm allows users to build split networks from distance measurements and has been implemented in various software such as SplitsTree.
Brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Anvi’o is an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. It empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.