Computational Framework for Biotechnological Research

Phylogenetic analysis

Phylogenetic analysis is the process to determine the evolutionary relationships between organisms. Phylogenetic trees determining evolutionary relationships includes matching patterns in nucleic acid and protein sequences.

Software Name Description
PHYLIP PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
PAML PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.
Batwing Phylogenetic Analysis (UNIX/LINUX Software)
Bayes Phylogenies The program allows a range of models of gene sequence evolution, models for morphological traits, models for rooted trees, gamma and beta distributed rate-heterogeneity, and implements a 'mixture model' (Pagel and Meade, 2004) that allows the user to fit more than one model of sequence evolution, without partitioning the data.
Bayes Traits The program allows a range of models of gene sequence evolution, models for morphological traits, models for rooted trees, gamma and beta distributed rate-heterogeneity, and implements a 'mixture model' (Pagel and Meade, 2004) that allows the user to fit more than one model of sequence evolution, without partitioning the data.
BEAST BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.
Bosque Gblocks is a tool for the selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.  It eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.
ClustalW ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences.
fastDNAml fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences.
Geneious This is useful for organize and analyze genomic and protein information via a single desktop program that provides publication ready images to enhance the impact of your research.
HyPhy HyPhy is a scriptable package that can fit statistical evolutionary models to alignment of homologous sequences using Maximum likelihood 2), estimate various parameters that have biological meaning, for example branch lengths, substitution rates, dN/dS ratios, recombination breakpoints, and test hypotheses about how sequences in the alignment have evolved.
IQPNNI An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees.
MEGA MEGA is an integrated tool for conducting automatic and manual sequence alignment,inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
Mesquite Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its.
MOLPHY Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks.
MrBayes MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem.
Network Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.
Nona Used to search for most parsimonious trees,used to calculate consensus trees, etc.,Extremely fast! In general, MUCH faster than competing software,WinClada is written to utilize NONA either directly as a search engine for phylogenetic analysis, or the two programs may be used separately.
SEMPHY SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.
Splits Tree SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.
TNT A simple, one-shot analysis is now included in the "" script, which comes with all TNT versions. This runs a simple analysis with a search for most parsimonious trees (or asks whether you want to do a consensus estimation, if the data set is large), then calculates group supports using resampling.
TreeGen Tree generation from distance data.
TreeFinder TREEFINDER computes phylogenetic trees from molecular sequences.
TREE-PUZZLE Maximum likelihood analysis for nucleotide, amino acid, and two-state data.
T-REX This program carries out a number of popular distance methods for the reconstruction of phylogenetix trees and reticulograms.
Winclada WinClada combines the features and functions of the older (DOS) programs DADA and CLADOS into a single program. CLADOS and DADA are no longer being distributed. If you are a user of DADA/CLADOS, and you have a Windows machine, you should migrate to WinClada.
Genomicus Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
Xrate Open-source package for phylogenetic comparative genomics. Its capabilities include maximum likelihood phylogeny, ancestral sequence reconstruction, alignment annotation and model estimation.