This method is used to find the evolutionary relationship between two or more sequences. It is also known as molecular systematic. It compares different organisms by finding distance between them and subsequently drawing the phylogenetic tree. The goal of the phylogenetic analysis is to develop phylogenetic tree depicting the hypothesis about the evolutionary ancestry of different sets of genes, species or other taxa.

Tool 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.

Phylogeny.fr

It is a simple to use web service for reconstructing and analyzing phylogenetic relationships between molecular sequences. It includes multiple alignment (MUSCLE, T-Coffee, ClustalW, ProbCons), phylogeny (PhyML, MrBayes, TNT, BioNJ), tree viewer (Drawgram, Drawtree, ATV) and utility programs (e.g. Gblocks to eliminate poorly aligned positions and divergent regions). (Reference: A. Dereeper et al,. 2008. Nucl. Acids Res. 36 (Web Server Issue):W465-9).

PHYML

It is accurate, fast and easy to use algorithm to estimate maximum likelihood phylogenies from DNA and protein sequences. This tool providesthe user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters. (Reference: S. Guindon et al. 2005. Nucl. Acids Res. 33: W557-W559).

ProtTest

Mac OSX, Windows and Linux versions are available for downloading. It estimates the empirical model of amino acid substitution that fits the data best among 64 candidate models.

Phylemon

a suite of web-tools for molecular evolution, phylogenetics and phylogenomics (H. Dopazo. Bioinformatics Department, Centro de Investigación Príncipe Felipe, Spain)

LVB:

It is abbreviated as Reconstructing Evolution with Parsimony and Simulated Annealing. LVB is based on unweighted reversible parsimony to reconstruct evolution which is based on a matrix of discrete characters for different objects such as aligned DNA sequences.

Phylodendron

It is also known as phylogenetic tree printer. Helps in visualizing dnd file from aligments and saving the results as .GIF, .PS or .PDF files. N.B. The output file can be altered in .PDF file.

CVTree

CVTree stands for Composition Vector. It was first developed to infer evolutionary relatedness of microbial organisms and then successfully applied to viruses, chloroplasts, and fungi. (Reference: Z. Xu & B. Hao 2009. Nucl. Acids Res. 37(Web Server issue:W174-W178)

POWER

It stands for PhylOgenetic Web Repeater.It is a user friendly interface. POWER provide two pipelines to process the analysis. One includes multiple sequence alignment (MSA) at the beginning and the other begin phylogenetic analysis with aligned sequence. (Reference: C.-Y. Lin. et al. 2005. Nucl. Acids Res. 33: W553-W556)