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mega [2008/05/20 14:25] – heidimega [2011/07/07 11:50] (current) – heidi
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 \\ \\
-Version 4 (May 1, 2008)\\+Version 5 (Aril 24, 2011)\\
 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 95/98, NT, 2000, XP, and Vista (with at least 64 MB of RAM, 20 MB of available hard disk space)+  * 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
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     * IG     * IG
     * Internet (NCBI) XML format     * Internet (NCBI) XML format
 +
  
  
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     * After the first character, taxa labels may contain the following additional special characters:''_, *, :, ( ), |, \, /''     * 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      * 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+++-_-+++---+++;
 </code> </code>
 +
  
  
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 === example === === example ===
 <code> <code>
-#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 +#Lagomorpha 
-            4.2+#Artiodactyla 
 +#Carnivora 
 +#Perissodactyla 
 +       
 +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
 </code> </code>
 +
  
  
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 ===== How to cite ===== ===== How to cite =====
-  * When referring to MEGA in the main text of your publication, you may choose a format such as:\\ +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 using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution doi: 10.1093/molbev/msr121. 
-  * When including a MEGA citation in the Literature Cited/Bibliography section, you may use the following:\\ +
-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. (Publication PDF at http://www.kumarlab.net/publications)+
  
 +\\
 +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.1211286328.txt.gz · Last modified: 2008/07/22 13:30 (external edit)