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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 buttonRead More
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FAQs on Lecture 15 - Molecular Phylogeny- Software for Phylogenetic Analyses - Bioinformatics - Botany
| 1. What is molecular phylogeny and why is it important in botany? |  |
Ans. Molecular phylogeny is the study of evolutionary relationships among organisms based on their genetic material, specifically DNA sequences. It is important in botany as it allows researchers to understand the evolutionary history and relatedness of different plant species. This information can be used to classify plants, identify common ancestors, and study the process of speciation.
| 2. What are some commonly used software for phylogenetic analyses in botany? | |
Ans. Some commonly used software for phylogenetic analyses in botany include:
1. MEGA (Molecular Evolutionary Genetics Analysis): It is a user-friendly software that allows researchers to conduct various analyses like sequence alignment, phylogenetic tree construction, and molecular evolutionary analysis.
2. PAUP* (Phylogenetic Analysis Using Parsimony): This software implements various algorithms for phylogenetic analysis, including maximum parsimony, maximum likelihood, and Bayesian inference.
3. MrBayes: It is a popular software for Bayesian phylogenetic inference that allows users to estimate phylogenetic trees and model parameters simultaneously.
4. BEAST (Bayesian Evolutionary Analysis Sampling Trees): This software is widely used for Bayesian analysis of molecular sequences to estimate divergence times and reconstruct phylogenetic trees.
5. PhyloBayes: It is a Bayesian software specifically designed for phylogenetic reconstruction using protein sequences.
| 3. How does molecular phylogeny differ from traditional taxonomy in botany? | |
Ans. Molecular phylogeny differs from traditional taxonomy in botany in the following ways:
1. Molecular phylogeny is based on genetic data, specifically DNA sequences, while traditional taxonomy relies on morphological characteristics.
2. Molecular phylogeny allows for a more accurate understanding of evolutionary relationships by comparing genetic similarities and differences, whereas traditional taxonomy primarily relies on observable physical traits.
3. Molecular phylogeny provides insights into the evolutionary history and relatedness of organisms, helping to uncover hidden relationships that may not be apparent through traditional taxonomy.
4. Molecular phylogeny can help resolve taxonomic controversies and clarify the classification of organisms by providing objective evidence of their evolutionary relationships.
| 4. Can molecular phylogeny be used to study the evolution of specific plant traits in botany? | |
Ans. Yes, molecular phylogeny can be used to study the evolution of specific plant traits in botany. By comparing DNA sequences and constructing phylogenetic trees, researchers can identify patterns of trait evolution and infer ancestral states. This can provide insights into the evolutionary origins of specific traits and how they have changed over time. Additionally, molecular phylogeny can help identify genes responsible for certain traits and study their evolutionary history. This information is valuable for understanding the genetic basis of plant traits and their adaptive significance.
| 5. What are the limitations of molecular phylogeny in botany? | |
Ans. Molecular phylogeny in botany has some limitations:
1. Availability of data: Molecular phylogeny relies on the availability of genetic data, specifically DNA sequences. In some cases, obtaining suitable DNA samples from certain plant species can be challenging, limiting the scope of analysis.
2. Mutational saturation: Over long periods of evolutionary time, DNA sequences can accumulate numerous mutations, making it difficult to accurately infer relationships. This is known as mutational saturation and can lead to errors in phylogenetic reconstruction.
3. Horizontal gene transfer: In some cases, genes can be transferred between different species, leading to incongruences in phylogenetic trees. Horizontal gene transfer can complicate the interpretation of evolutionary relationships.
4. Incomplete lineage sorting: During speciation events, ancestral genetic variation may not be completely sorted into descendant species, leading to conflicts between gene trees and species trees. This can make it challenging to resolve certain evolutionary relationships accurately.
5. Assumptions and models: Molecular phylogeny relies on various assumptions and models, such as assuming a constant rate of evolution or a specific evolutionary model. Violations of these assumptions or using inappropriate models can lead to biased or inaccurate results.
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