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HOME OLDER
VERSIONSTUTORIALFEATURESDOCUMENTATIONFEEDBACKWALK THROUGH MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. DOWNLOADS - MEGA SOFTWARE Notice: This version of MEGA X is an ALPHA test version that is intended to be used solely for testing purposes. Results produced using this version of MEGA X should not be used for publication.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. identifies a site as a singleton site if at least three sequences containunambiguous
CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
DAYHOFF AND JTT MODELS Dayhoff and JTT Models. The PAM and JTT distances correct for multiple substitutions based on the model of amino acid substitution described as substitution-rate matrices. TREE TOPOLOGY EDITOR Tree Topology Editor The tree topology editor shows a single trees topology in a way in which you are able to modify it. The toolset is very similar to the Tree Explorerࠀ, but ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections. CLUSTALW OPTIONS (PROTEIN) CLUSTALW Options (Protein) This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align DNA sequences. If you are aligning protein-coding sequences, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that you MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align.HOME OLDER
VERSIONSTUTORIALFEATURESDOCUMENTATIONFEEDBACKWALK THROUGH MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. DOWNLOADS - MEGA SOFTWARE Notice: This version of MEGA X is an ALPHA test version that is intended to be used solely for testing purposes. Results produced using this version of MEGA X should not be used for publication.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. identifies a site as a singleton site if at least three sequences containunambiguous
CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
DAYHOFF AND JTT MODELS Dayhoff and JTT Models. The PAM and JTT distances correct for multiple substitutions based on the model of amino acid substitution described as substitution-rate matrices. TREE TOPOLOGY EDITOR Tree Topology Editor The tree topology editor shows a single trees topology in a way in which you are able to modify it. The toolset is very similar to the Tree Explorerࠀ, but ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections. CLUSTALW OPTIONS (PROTEIN) CLUSTALW Options (Protein) This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align DNA sequences. If you are aligning protein-coding sequences, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that you MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align. MEGAX-HELP - MEGA SOFTWARE The ABI File Format is a binary file that is produced by ABI sequencer software. This data file, referred to as a “trace file” is viewable in MEGA’s Trace File Editor, which is part of the AlignmentExplorer.
SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. identifies a site as a singleton site if at least three sequences containunambiguous
MEGA - MOLECULAR EVOLUTIONARY GENETICS ANALYSIS MEGA Version : 1.0 : 2.x : 3.x : 4.x: Platform: DOS: Win: Win: Win: Input Data . DNA, Protein, Pairwise distance matrix • • • •Sequence Alignment
QUICK START TUTORIAL MEGA-CC Quick Start Tutorial. Example Data Files. For this tutorial, we will use example data files that are included with MEGA. When MEGA-GUI is launched for the first time, it will copy these example files to your computer in your Documents folder MOLECULAR EVOLUTIONARY GENETICS ANALYSIS Molecular Evolutionary Genetics Analysis Disclaimer Although the utmost care has been taken to ensure the correctness of the software, it is provided “as is,” without any warranty of any kind. TREE TOPOLOGY EDITOR Tree Topology Editor The tree topology editor shows a single trees topology in a way in which you are able to modify it. The toolset is very similar to the Tree Explorer , but with a few features added or removed.. The Topology Editor is also used during analyzes where the user is supplying their own tree. P-DISTANCE (NUCLEOTIDE) p-distance (Nucleotide) This distance is the proportion (p) of nucleotide sites at which two sequences being compared are different.It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared. BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree NEAREST-NEIGHBOR-INTERCHANGE (NNI) Nearest-Neighbor-Interchange (NNI) The Nearest-Neighbor-Interchange is a heuristic to improve the likelihood of a tree by performing the following operation on it. MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics and DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections.DEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align. MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics and DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections.DEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align. MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics andHOME
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets (Kumar, Stecher, and Tamura 2015). (2) When including a MEGA citation in the Literature Cited/Bibliography section BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics andDEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. TREE TOPOLOGY EDITOR Tree Topology Editor The tree topology editor shows a single trees topology in a way in which you are able to modify it. The toolset is very similar to the Tree Explorerࠀ, but P-DISTANCE (NUCLEOTIDE) p-distance (Nucleotide) This distance is the proportion ( p) of nucleotide sites at which two sequences being compared are different. It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared. It does not make any correction for multiple substitutions at the same site, substitution rate biases TAJIMA'S TEST OF NEUTRALITY Tajima's Test of Neutrality. Selection | Tajima’s Test of Neutrality. This conducts Tajima’s test of neutrality (Tajima 1989), which compares the number of segregating sites per site with the nucleotide diversity.(A site is considered segregating if, in a comparison of m sequences, there are two or more nucleotides at that site; nucleotide diversity is defined as the average number of CONSTRUCTING A TIME TREE (ML) Constructing a Time Tree (ML) This example shows how to use the Time Tree system in MEGA. The data files used in this example can be found in the MEGA/Example folder SUBTREE DRAWING OPTIONS (IN TREE EXPLORER) Subtree Drawing Options (in Tree Explorer) This dialog box provides choices options for changing various visual attributes for the selected subtree. If the Overwrite Downstream option is checked, any subtree drawing options that have been applied to downstream DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections.DEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align. MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics and DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA.SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li,ANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree ANALYSIS PREFERENCES (MAXIMUM LIKELIHOOD) Analysis Preferences (Maximum Likelihood) Analysis Preferences (ML) In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab.Available options are organized into logical sections.DEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align. MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics andHOME
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets (Kumar, Stecher, and Tamura 2015). (2) When including a MEGA citation in the Literature Cited/Bibliography section BOOTSTRAP TEST OF PHYLOGENY Bootstrap Test of Phylogeny. Phylogeny | Bootstrap Test of Phylogeny. One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree MEGA7: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS VERSION 7 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 forBiggerDatasets Sudhir Kumar,1,2,3 Glen Stecher1 and Koichiro Tamura*,4,5 1Institute for Genomics and Evolutionary Medicine, Temple University 2Department of Biology, Temple University 3Center for Excellence in Genome Medicine and Research , King Abdulaziz University, Jeddah, Saudi Arabia 4Research Center for Genomics andDEGENERACY
Degeneracy. 0-fold degenerate sites are those at which all changes are nonsynonymous. 2-fold degenerate sites are those at which one out of three changes is synonymous. (All sites at which two out of three changes are synonymous also are included in this category.) 4-fold degenerate sites are those at which all changes are synonymous. TREE TOPOLOGY EDITOR Tree Topology Editor The tree topology editor shows a single trees topology in a way in which you are able to modify it. The toolset is very similar to the Tree Explorerࠀ, but P-DISTANCE (NUCLEOTIDE) p-distance (Nucleotide) This distance is the proportion ( p) of nucleotide sites at which two sequences being compared are different. It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared. It does not make any correction for multiple substitutions at the same site, substitution rate biases TAJIMA'S TEST OF NEUTRALITY Tajima's Test of Neutrality. Selection | Tajima’s Test of Neutrality. This conducts Tajima’s test of neutrality (Tajima 1989), which compares the number of segregating sites per site with the nucleotide diversity.(A site is considered segregating if, in a comparison of m sequences, there are two or more nucleotides at that site; nucleotide diversity is defined as the average number of CONSTRUCTING A TIME TREE (ML) Constructing a Time Tree (ML) This example shows how to use the Time Tree system in MEGA. The data files used in this example can be found in the MEGA/Example folder SUBTREE DRAWING OPTIONS (IN TREE EXPLORER) Subtree Drawing Options (in Tree Explorer) This dialog box provides choices options for changing various visual attributes for the selected subtree. If the Overwrite Downstream option is checked, any subtree drawing options that have been applied to downstreamHOME OLDER
VERSIONSTUTORIALFEATURESDOCUMENTATIONFEEDBACKWALK THROUGH MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA. MEGAX-HELP - MEGA SOFTWAREMEGA MOLECULAR EVOLUTIONARY GENETICS ANAL…MEGA GENETICS In general, a composite likelihood is defined as a sum of log-likelihoods for related estimates. In MEGA4, the maximum composite likelihood is used for describing the sum of log-likelihoods for all pairwise distances in a distance matrix (Tamura et al. 2004) estimated by using the Tamura-Nei (1993) model (see related Tamura-Neidistance).
SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONSMEGA 10 SOFTWAREMEGA BIOLOGY SOFTWAREMEGA EVOLUTION SOFTWAREMEGA GENE Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li, MOLECULAR EVOLUTIONARY GENETICS ANALYSIS Molecular Evolutionary Genetics Analysis Disclaimer Although the utmost care has been taken to ensure the correctness of the software, it is provided “as is,” without any warranty of any kind.CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
CLUSTALW OPTIONS (PROTEIN) CLUSTALW Options (Protein) This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align DNA sequences. If you are aligning protein-coding sequences, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that youTREE LENGTH
Tree length. Tree length is the criterion used by the Maximum Parsimony method to search for the best tree. It is defined as the sum of the minimum numbers of substitutions over all sites for the given topology.. To compute the tree length for the unweighted parsimony method, we use the procedure described in Fitch (1971), which is based on the two rules described below. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align.HOME OLDER
VERSIONSTUTORIALFEATURESDOCUMENTATIONFEEDBACKWALK THROUGH MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. DOWNLOADS - MEGA SOFTWARE MEGA 11 (64-bit) ALPHA (for macOS) MEGA is provided FREE for use in research and education (see terms below) To download MEGA, please fill in the information requested below about how and where MEGA is used. This anonymous information is important for obtaining funding support for the maintenance and further development of MEGA. MEGAX-HELP - MEGA SOFTWAREMEGA MOLECULAR EVOLUTIONARY GENETICS ANAL…MEGA GENETICS In general, a composite likelihood is defined as a sum of log-likelihoods for related estimates. In MEGA4, the maximum composite likelihood is used for describing the sum of log-likelihoods for all pairwise distances in a distance matrix (Tamura et al. 2004) estimated by using the Tamura-Nei (1993) model (see related Tamura-Neidistance).
SINGLETON SITES
Singleton Sites. A singleton site contains at least two types of nucleotides (or amino acids) with, at most, one occurring multiple times. MEGA identifies a site as a singleton site if at least three sequences contain unambiguous nucleotides or amino acids. CITING MEGA IN PUBLICATIONSMEGA 10 SOFTWAREMEGA BIOLOGY SOFTWAREMEGA EVOLUTION SOFTWAREMEGA GENE Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms (Kumar, Stecher, Li, MOLECULAR EVOLUTIONARY GENETICS ANALYSIS Molecular Evolutionary Genetics Analysis Disclaimer Although the utmost care has been taken to ensure the correctness of the software, it is provided “as is,” without any warranty of any kind.CODON USAGE
Codon Usage. Statistics | Codon Usage. This command is visible only if the data contains protein-coding nucleotide sequences. MEGA computes the percent codon usage and the RCSU values for each codon for all sequences included in the dataset. Results will be displayed in by domain (if domains have been defined in Setup/Select Genes &Domains)..
CLUSTALW OPTIONS (PROTEIN) CLUSTALW Options (Protein) This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align DNA sequences. If you are aligning protein-coding sequences, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that youTREE LENGTH
Tree length. Tree length is the criterion used by the Maximum Parsimony method to search for the best tree. It is defined as the sum of the minimum numbers of substitutions over all sites for the given topology.. To compute the tree length for the unweighted parsimony method, we use the procedure described in Fitch (1971), which is based on the two rules described below. MUSCLE OPTIONS (PROTEIN) MUSCLE Options (Protein) This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align.HOME
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. INSTRUCTIONAL VIDEOS The first section of videos were created by members of Dr. Sudhir Kumar's lab at the Institute for Genomics and Evolutionary Medicine ( iGEM) at Temple University. The rest of the videos were produced by users of MEGA. To assemble this collection of videos, the MEGA team performed a search of YouTube for instructional MEGA videos andassembled
MOLECULAR EVOLUTIONARY GENETICS ANALYSIS Molecular Evolutionary Genetics Analysis Disclaimer Although the utmost care has been taken to ensure the correctness of the software, it is provided “as is,” without any warranty of any kind. CONTENTS --MEGA MANUAL 7. Walk through MEGA. 7.1 Constructing Trees from Distance Data. 7.2 Computing Statistical Quantities for Nucleotide Sequences. 7.3 Estimating Evolutionary Distances from Nucleotide Sequences. 7.4 Constructing Trees and Selecting OTUS from Nucleotide Sequences. 7.5Tests of
CITING MEGA IN PUBLICATIONS Citing MEGA in Publications. If you wish to cite MEGA in your publications, we suggest the following: (1) When referring to MEGA in the main text of your publication, you may choose a format such as:. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets (Kumar, Stecher, and Tamura 2015). (2) When including a MEGA citation in the Literature Cited/Bibliography sectionANALYSIS OPTIONS
Analysis Options. In this dialog box you can select and view desired options in the Options Summary.Options are organized in logical sections. A yellow row indicates that you have a choice for that particular attribute. The primary sets of options available in thisdialog box are:
CLUSTALW OPTIONS (PROTEIN) CLUSTALW Options (Protein) This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align DNA sequences. If you are aligning protein-coding sequences, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that you MEGAX-HELP - MEGA SOFTWARE MEGAX-Help % End of search results. NEAREST-NEIGHBOR-INTERCHANGE (NNI) Nearest-Neighbor-Interchange (NNI) The Nearest-Neighbor-Interchange is a heuristic to improve the likelihood of a tree by performing the following operation on it. TAJIMA'S TEST OF NEUTRALITY Tajima's Test of Neutrality. Selection | Tajima’s Test of Neutrality. This conducts Tajima’s test of neutrality (Tajima 1989), which compares the number of segregating sites per site with the nucleotide diversity.(A site is considered segregating if, in a comparison of m sequences, there are two or more nucleotides at that site; nucleotide diversity is defined as the average number of* tutorial
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TESTERS NEEDED FOR MEGA11 (ALPHA) FOR WINDOWS, LINUX, AND MACOS! Version 11.0 has a new memory-efficient ML engine, updated Tree Explorer, and many other enhancements. SOPHISTICATED AND USER-FRIENDLY SOFTWARE SUITE FOR ANALYZING DNA AND PROTEIN SEQUENCE DATA FROM SPECIES AND POPULATIONS. MEGA X: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS ACROSS COMPUTINGPLATFORMS
Version 10 of the MEGA software enables cross-platform use, running natively on Windows and Linux systems. MOLECULAR EVOLUTIONARY GENETICS ANALYSIS (MEGA) FOR MACOS MEGA X for macOS 10.13 (High Sierra) and newer runs natively using theCocoa widget set.
MEGA SOFTWARE CELEBRATES SILVER ANNIVERSARY In the past 25 years, the MEGA software has been downloaded more then 1.6 million times... INSTRUCTIONAL VIDEOS NOW AVAILABLE Learn how to use MEGA from video tutorials created by MEGA users.*
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