mega
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- | Version | + | Version |
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. | 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. | ||
+ | |||
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===== Program information ===== | ===== Program information ===== | ||
- | * Windows | + | * Windows XP, Vista, 7 (with at least 64 MB of RAM, 20 MB of available hard disk space) |
* MEGA also can be run on other operating systems for which Windows emulators are available: | * MEGA also can be run on other operating systems for which Windows emulators are available: | ||
* Macintosh: Windows using VirtualPC | * Macintosh: Windows using VirtualPC | ||
* Sun Workstation: | * Sun Workstation: | ||
* Linux: Windows using VMWare | * Linux: Windows using VMWare | ||
+ | |||
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* RNA | * RNA | ||
* nucleotide | * nucleotide | ||
+ | * distance | ||
* (protein sequences) | * (protein sequences) | ||
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* IG | * IG | ||
* Internet (NCBI) XML format | * Internet (NCBI) XML format | ||
+ | |||
+ | |||
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\\ | \\ | ||
- | * Comments: | + | * Comments: |
- | * keywords: | + | * anywhere in the data file |
- | * Rules for Taxa Names: Distance matrices as well as sequence data may come from species, populations, | + | * can span multiple lines |
- | * ‘#’ Sign: Every Iabel must be written on a new line, and a '#' | + | * enclosed in square brackets ([and]) |
- | * Characters: Taxa labels | + | * can be nested |
+ | * keywords: | ||
+ | * written in any combination of lower- and upper-case letters | ||
+ | * Taxa Names: | ||
+ | * ‘#’ Sign: Every Iabel must be written on a new line, and a '#' | ||
+ | * no restrictions on the length of the Iabels | ||
+ | * not required to be unique | ||
+ | * must start with alphanumeric characters (0-9, a-z, and A-Z) or a special character: '' | ||
+ | * After the first character, taxa labels may contain the following additional special characters:'' | ||
+ | * For multiple word labels, an underscore can be used to represent a blank space | ||
+ | |||
+ | \\ | ||
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* there should be no spaces between the taxa name and group name | * there should be no spaces between the taxa name and group name | ||
- | * **Labelling Individual Sites:**¨ | + | * **Labelling Individual Sites:** |
* The individual sites in nucleotide or amino acid data can be labeled to construct non-contiguous sets of sites. | * The individual sites in nucleotide or amino acid data can be labeled to construct non-contiguous sets of sites. | ||
* Each site can be associated with only one label | * Each site can be associated with only one label | ||
- | * A label can be a letter or a | + | * A label can be a letter or a number. |
- | number. | + | |
=== example === | === example === | ||
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!Label +++__-+++-a-+++-L-+++-k-+++123+++-_-+++---+++; | !Label +++__-+++-a-+++-L-+++-k-+++123+++-_-+++---+++; | ||
</ | </ | ||
+ | |||
+ | |||
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* **Keywords for Format Statement: | * **Keywords for Format Statement: | ||
- | ^ Command ^ Setting ^ Remark ^ Example ^ | + | ^ Command ^ Setting ^ Remark ^ Example ^ |
- | | DataType | DNA, RNA, nucleotide, protein | + | | DataType | Distance |
- | | NSeqs | integer | Number of sequences | NSeqs=85 | | + | | NSeqs | integer | Number of sequences | NSeqs=85 | |
- | | NTaxa | integer | Synonymous with NSeqs | NTaxa=85 | | + | | NTaxa | integer | Same as NSeqs | NTaxa=85 | |
- | | NSites | + | | DataFormat |
- | | Property | Exon, Intron, Coding, Noncoding, and End | Specifies whether | + | |
- | | Indel | single character | Use dash (-) | Indel = - | | + | |
- | | Identical | single character | Use period (.) | Identical = . | | + | |
- | | MatchChar | single character | Synonymous with identical | MatchChar = . | | + | |
- | | Missing | single character | Use a question mark (?) | Missing = ? | | + | |
- | | CodeTable | A name | This instruction gives the name of the code table for the protein coding domains of the data | CodeTable = Standard | | + | |
* **Defining Groups:** | * **Defining Groups:** | ||
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=== example === | === example === | ||
< | < | ||
- | #one | + | #mega |
- | #two | + | !Title: Concatenated Files; |
- | #three | + | !Format DataType=Distance DataFormat=LowerLeft NTaxa=6; |
- | #four | + | |
- | #five | + | |
- | 1.0 2.0 3.0 4.0 | + | #Rodent |
- | 3.0 2.5 4.6 | + | #Primate |
- | 1.3 3.6 | + | # |
- | 4.2 | + | # |
+ | # | ||
+ | # | ||
+ | |||
+ | 0.514 | ||
+ | 0.535 0.436 | ||
+ | 0.530 0.388 0.418 | ||
+ | 0.521 0.353 0.417 0.345 | ||
+ | 0.500 0.331 0.402 0.327 0.349 | ||
</ | </ | ||
+ | |||
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===== How to cite ===== | ===== How to cite ===== | ||
- | * When referring to MEGA in the main text of your publication, | + | Citation for MEGA 5: |
- | Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 4 (Tamura, Dudley, Nei, and Kumar 2007). | + | * Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis |
- | * When including a MEGA citation in the Literature Cited/ | + | |
- | Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis | + | |
+ | \\ | ||
+ | Citation for MEGA 4: | ||
+ | * Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599. |
mega.1211277221.txt.gz · Last modified: 2008/07/22 13:30 (external edit)