Bioinformatics Assignment Topic: Phylogenetics Analysis Softwares
Bioinformatics Assignment Topic: Phylogenetics Analysis Softwares
TOPIC
PHYLOGENETICS ANALYSIS SOFTWARES
NAME – NIDHI
CONTENTS
INTRODUCTION
Phylogenetics analysis software
•PAUP*
•PHYLIP
•TREE-PUZZEL
•PYML
•MEGA
•Mr BAYES
Reference
INTRODUCTION
Phylogenetics is the study of the evolutionary relationship history of living
organism using tree like diagram to represent pedigrees if these organism. The
tree branching patterns representing the evolutionary divergence are referred to
as phylogeny. There are currently two main categories of tree building methods,
each having advantages and disadvantages. The first category is on discrete
characters, which are molecular sequence from individual taxa. The basic
assumption is that characters at corresponding positions in multiple sequence
alignment are homologous among the sequence required. Therefore, the character
states of the common ancestor can be traced from these dataset.
The second category of phylogenetic methods is based on distance, which is the
amount of dissimilarities between pairs of sequences, computed on the basis of
sequence alignment. The distance based method assumes that all sequence
involved are homologous and that tree branches are additive.
Phylogenetic tree construction is not a trivial task as numerous phylogenetic
programs are available. These programmes are freely available. Some are
comprehensive packages, others are more specialized to perform a single task.
Phylogenetics analysis software or programmes
The advantage is that it allow various substitution models for likelihood score
estimation and incorporates a discrete ẟ model for rate heterogeneity among
sites. Because of the heuristic nature of the program , it allows ML analysis of
large datasets. The resulting puzzle trees are automatically assigned PUZZEL
support values to internal branches. These values are percentage of consistent
quartet trees and do not have the same meaning as bootstrap values.
TREE-PUZZEL 5.0 is available for Mac, UNIX, and Windows and can be
downloaded from www.tree-puzzeel.de/. There is also online version of the
program is available at http://bioweb.pasteu.fr/seqanal/interfaces/Puzzel.html.
PYML (http://atgc.lirmm.fr/phyml/) is a web based phylogenetics program using
the GA . it first builds as NJ tree and uses it as a starting tree for subsequent
iterative refinement through subtree swapping. Branch lengths are
simultaneously optimized during this process .The tree searching stops when the
total ML score no longer increases. The main advantage of this program is the
ability to build trees from very large datasets with hundreds of taxa and to
complete tree searching within a relatively short time frame.
PHYML Online is a web interface to PHYML, a software that implements a fast
and accurate heuristic for estimating maximum likelihood phylogenies from
DNA and protein sequences. This tool provides the user with a number of options,
e.g. nonparametric bootstrap and estimation of various evolutionary parameters,
in order to perform comprehensive phylogenetic analyses on large datasets in
reasonable computing time.
MEGA (Molecular Evolutionary Genetic Analysis) is produced by Sudhir
Kumar of the Centre for Evolutionary Functional Genomics of the The
Biodesign Institute at Arizona State University, Tempe, Arizona together with
Joel Dudley of the Stanford Centre for Biomedical Informatics Research at
Stanford University, Koichiro Tamura of Tokyo Metropolitan University and
Masatoshi Nei, of Pennsylvania State University. It carries out parsimony,
distance matrix and likelihood methods for molecular data (nucleic acid
sequences and protein sequences). It can do boostrapping, consensus trees, and
a variety of distance measures, with Neighbor-Joining, Minimum Evolution,
UPGMA, and parsimony tree methods, as a well as a large variety of data
editing tasks, sequence alignment using an implementation of ClustalW, tests of
the molecular clock, and single-branch tests of significance of groups. MEGA4
is the current version.
MEGA has been updated and expanded several times and currently all these
versions are available from the MEGA website. The latest release, MEGA7, has
been optimized for use on 64-bit computing systems. MEGA is in two version.
A graphical user interface is available as a native Microsoft Windows program.
A command line version, MEGA-Computing Core (MEGA-CC), is available
for native cross-platform operation. The method is widely used and cited. With
millions of downloads across the releases, MEGA is cited in more than 85,000
papers. The 5th version has been cited over 25,000 times in 4 years.
Mr BAYES is a Bayesian phylogenetic inference program.
It randomly samples tree topologies using the MCMC procedure and the
posterior distribution of tree topologies. It has a range of probabilistic models
available to search for a set of trees with the highest posterior probability.
It is fast and capable of handling large datasets. The program is available in
multiplatform versions and can be downloaded from
http://morphbank.ebc.uu.se/mrbayes/.
A web program that also employs Bayesian inference for phylogenetic analysis
is BAMBE (http://bioweb.pasteur.fr/seqanal/interfaces/bambe.html)