BIOINFORMATICS ASSIGNMENT

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

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a

program for phylogenetic analysis using parsimony, maximum likelihood, and
distance methods by David Swofford in 2003. It is a commercial phylogenetic
package , http://paup.csit.fsu.edu/ . It is probably one of the widely used
phylogenetic programs available from Sinauer Publishers.
It is a Macintosh program ,PowerMac, windows and UNIX/open VMS versions
with user friendly graphical interface.It is one of the most sophisticated
parsimony program, with many options and close compatibility with MacClade.it
has become much broader with inclusion of more methods. PAUP was originally
developed as a parsimony program but expanded to a comprehensive package
that is capable of performing distance, parsimony, and likelihood analysis. The
distance option include NJ, ME ,FM and UPGMA. For distance or ML analysis,
PAUP has the option for detailed specifications of substitution models, base
frequencies and among site rate heterogeneity. It is also able to perform
nonparametric bootstrapping, jackknifing, KH testing and SH testing.
PHYLIP (Phylogenetics interference program) :-
PHYLIP is a free package of programs for inferring
phylogenies by Joe Felsenstein. It is distributed as
source code, documentation files, and a number of
different types of executables.
It is multiplatform comprehensive package containing
thirty-five subprograms for performing distance,
parsimony, and likelihood analysis as well as bootstrapping for both nucleotide
and amino acid sequences. It is command like based , but relatively easy to use
for each single program. PHYLIP version 3.6 package is available free, from its
Web site, in C source code, or as executables for Windows, Mac OS X, and
Mac OS 8 or 9. The C source code can easily be compiled on Unix or Linux
systems.
The only problem is that to complete an analysis the user is required to move
between different subprograms while keeping modifying names of the
intermediate modified files. The program package is downloaded from
http://evolution.genetics.washington.edu/phylip.html.
An online version is also available at
http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html.
A more user friendly version is webPhylip.
TREE-PUZZEL is a program performing quartet puzzling. Heiko Schmidt,
Korbinian Strimmer and Arndt von Haeseler have developed TREE-
PUZZLE version 5.2, (formerly called PUZZLE) a program for maximum
likelihood analysis for nucleotide and amino acid alignments. TREE-PUZZLE
infers phylogenies by "quartet puzzling", a method that applies maximum
likelihood tree reconstruction to all possible quartets of taxa and subsequently
tries to combine most of the four-taxa maximum likelihood trees to construct an
overall maximum likelihood tree. Usually there are several possible solutions. A
consensus tree generated from the quartet puzzling trees shows nodes that are
well supported.

TREE-PUZZLE supports all popular models of sequence evolution of

nucleotides and proteins, and can take rate heterogeneity among sites into
account. It computes pairwise maximum likelihood distances for many different
models of sequence evolution (TN, HKY, F84, SH, Dayhoff, JTT, mtREV24,
BLOSUM62, WAG, and VT), and estimates parameters of the models. It can
estimate maximum-likelihood branch-lengths for user-specified trees and
perform likelihood ratio tests of clockness as well as Kishino-Hasegawa-
Templeton tests. The program is written in ANSI C and is compatible with
PHYLIP files. The current version also has features for parallel computation
using the MPI message-passing interface, if this is available. Precompiled
executables are distributed for Mac OS, Windows, and Linux. For Unix and VMS
systems files for automated compilation are provided. A version capable of
parallel execution is also available.

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)

Program features include:

 A common command-line interface across Macintosh, Windows, and
UNIX operating systems;
 Extensive help available from the command line;
 Analysis of nucleotide, amino acid, restriction site, and morphological
data;
 Mixing of data types, such as molecular and morphological characters, in
a single analysis;
 Easy linking and unlinking of parameters across data partitions;
 An abundance of evolutionary models, including 4x4, doublet, and codon
models for nucleotide data and many of the standard rate matrices for
amino acid data;
 Estimation of positively selected sites in a fully hierarchical Bayesian
framework;
 Full integration of the BEST algorithms for the multi-species coalescent;
 Support for complex combinations of positive, negative, and backbone
constraints on topologies;
 Model jumping across the GTR model space and across fixed rate matrices
for amino acid data;
 Monitoring of convergence during the analysis, and access to a wide range
of convergence diagnostics tools after the analysis has finished;
 Rich summaries of posterior samples of branch and node parameters
printed to majority rule consensus trees in FigTree format;
 Implementation of the stepping-stone method for accurate estimation of
model likelihoods for Bayesian model choice using Bayes factors;
 The ability to spread jobs over a cluster of computers using MPI (for
Macintosh (OS X) and UNIX environments only);
 Support for the BEAGLE library, resulting in dramatic speedups for codon
and amino acid models on compatible hardware (NVIDIA graphics cards);
 Check pointing across all models, allowing the user to seamlessly extend a
previous analysis or recover from a system crash.
List of phylogenetics software
Reference
Essential bioinformatics by Jin Xiong
http://evolution.genetics.washington.edu/phylip/software.html
http://nbisweden.github.io/MrBayes/