A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.
Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. It contains classes to represent biological sequences and sequence annotations, and it is able to read and write to a variety of file formats. It also allows for a programmatic means of accessing online databases of biological information, such as those at NCBI. Separate modules extend Biopython's capabilities to sequence alignment, protein structure, population genetics, phylogenetics, sequence motifs, and machine learning. Biopython is one of a number of Bio* projects designed to reduce code duplication in computational biology.
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. Several popular phylogenetic programs such as PAUP*, MrBayes, Mesquite, MacClade and SplitsTree use this format.
The ARB Project is a free software package for the phylogenetic analysis of rRNA and other biological sequences including DNA and protein sequence. It simplifies the import and assembly of genetic sequences from any organisms with the use of an automated aligner. This editing process can be depicted into two subcategories: "Primary Structure Editor" and "Secondary Structure Editor". Comprehensively, this allows the necessary make up for developing a phylogenetic tree. The software provides the visualization of the biological sequences which gives the user a more in depth experience and interaction. This is particularly necessary when comparing phylogeny data from various organisms.
The system safety concept calls for a risk management strategy based on identification, analysis of hazards and application of remedial controls using a systems-based approach. This is different from traditional safety strategies which rely on control of conditions and causes of an accident based either on the epidemiological analysis or as a result of investigation of individual past accidents. The concept of system safety is useful in demonstrating adequacy of technologies when difficulties are faced with probabilistic risk analysis. The underlying principle is one of synergy: a whole is more than sum of its parts. Systems-based approach to safety requires the application of scientific, technical and managerial skills to hazard identification, hazard analysis, and elimination, control, or management of hazards throughout the life-cycle of a system, program, project or an activity or a product. "Hazop" is one of several techniques available for identification of hazards.
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree implements published methods such as split decomposition, neighbor-net, consensus networks, super networks methods or methods for computing hybridization or simple recombination networks. It uses the NEXUS file format. The splits graph is defined using a special data block.
MEGAN is a computer program that allows optimized analysis of large metagenomic datasets.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics. Besides tree description formats with limited expressiveness, it also implements the phyloXML format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV).
Quantitative comparative linguistics is the use of quantitative analysis as applied to comparative linguistics. Examples include the statistical fields of lexicostatistics and glottochronology, and the borrowing of phylogenetics from biology.
For a given set of taxa like X, and a set of splits S on X, usually together with a non-negative weighting, which may represent character changes distance, or may also have a more abstract interpretation, if the set of splits S is compatible, then it can be represented by an unrooted phylogenetic tree and each edge in the tree corresponds to exactly one of the splits. More generally, S can always be represented by a split network, which is an unrooted phylogenetic network with the property that every split s in S is represented by an array of parallel edges in the network.
The Open Tree of Life is an online phylogenetic tree of life – a collaborative effort, funded by the National Science Foundation. The first draft, including 2.3 million species, was released in September 2015. The Interactive graph allows the user to zoom in to taxonomic classifications, phylogenetic trees, and information about a node. Clicking on a species will return its source and reference taxonomy.
Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to MacClade, when the authors recognized that implementing a modular architecture in MacClade would be infeasible. Mesquite is largely written in Java and uses NEXUS-formatted files as input. Mesquite is available as a compiled executable for Macintosh, Windows, and Unix-like platforms, and the source code is available on GitHub.
ADMIXTOOLS is a software package that is primarily used for analyzing admixture in population genetics. The original version was developed as a set of standalone C programs by Nick Patterson and colleagues and published in 2012. A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.
