Page 1
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 0
Subject: Bioinformatics
Lesson: Molecular Phylogeny- Software for Phylogenetic Analyses
Lesson Developer: Shailendra Goel
College/ Department: Department of Botany, University of Delhi
Page 2
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 0
Subject: Bioinformatics
Lesson: Molecular Phylogeny- Software for Phylogenetic Analyses
Lesson Developer: Shailendra Goel
College/ Department: Department of Botany, University of Delhi
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: Software for Phylogenetic Analyses
? Introduction
? Program MEGA
? Opening files
? Launching tool bar
? How to USE MEGA
? Tree Explorer
? Program TreeView
? Introduction
? Manual for TreeView
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
Page 3
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 0
Subject: Bioinformatics
Lesson: Molecular Phylogeny- Software for Phylogenetic Analyses
Lesson Developer: Shailendra Goel
College/ Department: Department of Botany, University of Delhi
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: Software for Phylogenetic Analyses
? Introduction
? Program MEGA
? Opening files
? Launching tool bar
? How to USE MEGA
? Tree Explorer
? Program TreeView
? Introduction
? Manual for TreeView
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 2
Introduction
Various Programs are available which use different methods for constructing phylogenetic
trees. Some of the most popular software are listed below:
1. PAUP (Phylogenetic Analysis Using Parsimony): Developed by David Swofford, this is
a versatile program for maximum parsimony based tree construction. This is a
commercial package. This program, for a long time had been the popular tool for
phylogenetic construction. It has a two versions – Macintosh platform version and
Windows version. Macintosh Platform version is user friendly version using pull down
menu interface. Windows version is a command line version and is although powerful
but is not only comparatively difficult to use but is also bug ridden. Still, due to its
versatility, it is still used for phylogenetic study.
2. MEGA (Molecular Genetic Evolutionary Analysis) by Sudhir Kumar, Koichiro Tamura
and Masatoshi Nei. Running into it’s fifth version, program is available for both
Macintosh and Windows platforms. It comes with both user friendly interface and
also command line interface. Having an intuitive interface, it is an easy to use
program.
3. PHYLIP (Phylogeny Inference Package) by Joseph Felsenstein. It is not one program
but a package of many standalone programs. This is one of the versatile packages
being used widely. The program comes with a comprehensive manual and is a very
good resource to start experimenting with phylogeny.
4. DARwin by Xavier Perrier & Jean-Pierre Jacquemond-Collet is a program developed
by CIRAD under generation challenge program. It uses distance methods for
diversity analysis using different kinds of datasets including DNA sequences.
5. MrBayes by John Huelsenbeck and Fredrik Ronquist is a program which uses
Bayesian method for phylogenetic reconstruction.
All these programs generate trees which can be viewed by one versatile program called
“TreeView”. This is a useful program by Roderick D. M. Page. We will focus on two programs
here, MEGA and TreeView.
Program MEGA
Opening files
Page 4
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 0
Subject: Bioinformatics
Lesson: Molecular Phylogeny- Software for Phylogenetic Analyses
Lesson Developer: Shailendra Goel
College/ Department: Department of Botany, University of Delhi
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: Software for Phylogenetic Analyses
? Introduction
? Program MEGA
? Opening files
? Launching tool bar
? How to USE MEGA
? Tree Explorer
? Program TreeView
? Introduction
? Manual for TreeView
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 2
Introduction
Various Programs are available which use different methods for constructing phylogenetic
trees. Some of the most popular software are listed below:
1. PAUP (Phylogenetic Analysis Using Parsimony): Developed by David Swofford, this is
a versatile program for maximum parsimony based tree construction. This is a
commercial package. This program, for a long time had been the popular tool for
phylogenetic construction. It has a two versions – Macintosh platform version and
Windows version. Macintosh Platform version is user friendly version using pull down
menu interface. Windows version is a command line version and is although powerful
but is not only comparatively difficult to use but is also bug ridden. Still, due to its
versatility, it is still used for phylogenetic study.
2. MEGA (Molecular Genetic Evolutionary Analysis) by Sudhir Kumar, Koichiro Tamura
and Masatoshi Nei. Running into it’s fifth version, program is available for both
Macintosh and Windows platforms. It comes with both user friendly interface and
also command line interface. Having an intuitive interface, it is an easy to use
program.
3. PHYLIP (Phylogeny Inference Package) by Joseph Felsenstein. It is not one program
but a package of many standalone programs. This is one of the versatile packages
being used widely. The program comes with a comprehensive manual and is a very
good resource to start experimenting with phylogeny.
4. DARwin by Xavier Perrier & Jean-Pierre Jacquemond-Collet is a program developed
by CIRAD under generation challenge program. It uses distance methods for
diversity analysis using different kinds of datasets including DNA sequences.
5. MrBayes by John Huelsenbeck and Fredrik Ronquist is a program which uses
Bayesian method for phylogenetic reconstruction.
All these programs generate trees which can be viewed by one versatile program called
“TreeView”. This is a useful program by Roderick D. M. Page. We will focus on two programs
here, MEGA and TreeView.
Program MEGA
Opening files
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 3
MEGA can be downloaded for free from the website: Source:
http://www.megasoftware.net/index.php. MEGA comes with an alignment editor which can
handle alignments created with other programs like CLUSTALX. The alignment is opened in
“alignment explorer”. Alignment explorer can open already aligned sequences in NEXUS,
CLUSTALX, MEGA and many other formats. The option “convert” can convert the file format
to “mega” which is read and processed by program. The program can also align sequences
using “ClustalW” or “MUSCLE” option. If a file intended to be used by program in different
file format has error, it open in text editor automatically so that user can see the error and
correct it.
Launching tool bar:
When you open the program it first shows the launching toolbar. Launching toolbar
gives you an idea about the things which can be done with this program. Besides aligning
sequences and creating tree using different methods program can also do some useful
statistical analysis of phylogenetic significance. Some of these analyses include basic
analysis like nucleotide frequencies, codon frequencies, and transition/transversion ratios.
There are various options of models for calculating distance. Program presently does not
have option to calculate gamma parameter but if provided gamma parameter value, can
calculate gamma distances. For more understanding, one should go through the help file.
Here we will only do simple exercise which will include using an alignment file for
creating Neighbor joining tree, Maximum parsimony tree and Maximum likelihood tree.
How to USE MEGA
Page 5
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 0
Subject: Bioinformatics
Lesson: Molecular Phylogeny- Software for Phylogenetic Analyses
Lesson Developer: Shailendra Goel
College/ Department: Department of Botany, University of Delhi
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: Software for Phylogenetic Analyses
? Introduction
? Program MEGA
? Opening files
? Launching tool bar
? How to USE MEGA
? Tree Explorer
? Program TreeView
? Introduction
? Manual for TreeView
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 2
Introduction
Various Programs are available which use different methods for constructing phylogenetic
trees. Some of the most popular software are listed below:
1. PAUP (Phylogenetic Analysis Using Parsimony): Developed by David Swofford, this is
a versatile program for maximum parsimony based tree construction. This is a
commercial package. This program, for a long time had been the popular tool for
phylogenetic construction. It has a two versions – Macintosh platform version and
Windows version. Macintosh Platform version is user friendly version using pull down
menu interface. Windows version is a command line version and is although powerful
but is not only comparatively difficult to use but is also bug ridden. Still, due to its
versatility, it is still used for phylogenetic study.
2. MEGA (Molecular Genetic Evolutionary Analysis) by Sudhir Kumar, Koichiro Tamura
and Masatoshi Nei. Running into it’s fifth version, program is available for both
Macintosh and Windows platforms. It comes with both user friendly interface and
also command line interface. Having an intuitive interface, it is an easy to use
program.
3. PHYLIP (Phylogeny Inference Package) by Joseph Felsenstein. It is not one program
but a package of many standalone programs. This is one of the versatile packages
being used widely. The program comes with a comprehensive manual and is a very
good resource to start experimenting with phylogeny.
4. DARwin by Xavier Perrier & Jean-Pierre Jacquemond-Collet is a program developed
by CIRAD under generation challenge program. It uses distance methods for
diversity analysis using different kinds of datasets including DNA sequences.
5. MrBayes by John Huelsenbeck and Fredrik Ronquist is a program which uses
Bayesian method for phylogenetic reconstruction.
All these programs generate trees which can be viewed by one versatile program called
“TreeView”. This is a useful program by Roderick D. M. Page. We will focus on two programs
here, MEGA and TreeView.
Program MEGA
Opening files
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 3
MEGA can be downloaded for free from the website: Source:
http://www.megasoftware.net/index.php. MEGA comes with an alignment editor which can
handle alignments created with other programs like CLUSTALX. The alignment is opened in
“alignment explorer”. Alignment explorer can open already aligned sequences in NEXUS,
CLUSTALX, MEGA and many other formats. The option “convert” can convert the file format
to “mega” which is read and processed by program. The program can also align sequences
using “ClustalW” or “MUSCLE” option. If a file intended to be used by program in different
file format has error, it open in text editor automatically so that user can see the error and
correct it.
Launching tool bar:
When you open the program it first shows the launching toolbar. Launching toolbar
gives you an idea about the things which can be done with this program. Besides aligning
sequences and creating tree using different methods program can also do some useful
statistical analysis of phylogenetic significance. Some of these analyses include basic
analysis like nucleotide frequencies, codon frequencies, and transition/transversion ratios.
There are various options of models for calculating distance. Program presently does not
have option to calculate gamma parameter but if provided gamma parameter value, can
calculate gamma distances. For more understanding, one should go through the help file.
Here we will only do simple exercise which will include using an alignment file for
creating Neighbor joining tree, Maximum parsimony tree and Maximum likelihood tree.
How to USE MEGA
Molecular Phylogeny- Software for Phylogenetic Analyses
Institute of Lifelong Learning, University of Delhi 4
Mega is a menu driven phylogeny program. We will use this program to create Neighbor Joining
tree, Maximum Parsimony and Maximum Likelihood trees. We will first open the data file
generated by ClustalX and convert it into MEGA format.
Input file : Open the data file.
Source: http://www.megasoftware.net/index.php
After you open the data file, your menu changes and you get an option to convert to mega
format. If you minimize window and enlarge again, you get the original window. To get back
to data window click data button
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