The task of resolving the tree of life of extant species remains one of the grand challenges in evolutionary biology. As the number of trees grows superexponentially with the number of species for which an evolutionary tree is reconstructed, tree inference is considered a hard problem in computer science. The plethora of algorithmic challenges associated with phylogenetic trees and their efficient computation gave rise to the discipline of “phyloinformatics.”
Assists users to observe DNA and protein sequence data from different species and populations. MEGA is composed of several tools allowing researchers to work on phylogenomics and phylomedicine. This repository includes features aiming to determine gene duplication events in gene family trees. Moreover, this tool is available through a graphical user interface (GUI) and a command line interface.
Manages and manipulates life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. It is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists. It provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project.
Uses maximum likelihood inference to simultaneously detect recombination in whole genome datasets and account for it in phylogenetic reconstruction. ClonalFrame can analyse hundreds of genomes in a matter of hours. This tool demonstrates its ability to estimate recombination parameters and detect importation events in the context of understanding short-term transmission dynamics and long-term evolution.
Constructs large phylogenies and estimates their reliability. FastTree uses nearest-neighbor interchanges (NNIs), the minimum-evolution criterion, minimum-evolution subtree-pruning-regrafting (SPRs) and maximumlikelihood NNIs to improve the tree. It uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
Assists in selecting DNA substitution models using the PAUP* program. MrModeltest is an application that performs hierarchical likelihood ratio tests. It also calculates approximate Akaike information criterion (AIC) values of the nucleotide substitution models. This method is a modified version of the Modeltest software.
A web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. ConSurf combines two independent servers (ConSeq and ConSurf), providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences.