MEGA
documentation

Version 4 (May 1, 2008)
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.

• Windows 95/98, NT, 2000, XP, and Vista (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:
  • Macintosh: Windows using VirtualPC
  • Sun Workstation: SoftWindows95
  • Linux: Windows using VMWare

• DNA
• RNA
• nucleotide
• (protein sequences)

• ASCII-text files
• extension: *.MEG

• first line: must contain the keyword #MEGA
• second line: data file may contain a succinct description of the data (called Title). The Title statement is written according to a set of rules:
  • always begins with !Title and ends with a semicolon
  • not occupy more than one line of text
  • must not contain a semicolon inside the statement
  • example:

    #mega
    !Title This is an example title;

• third line: Description statement: more descriptive multi-line account of the data.
  • always begins with !Description and ends with a semicolon
  • may occupy multiple lines
  • must not contain a semicolon inside the statement
  • example:

    #mega
    !Title This is an example title;
    !Description This is detailed information the data file;

• Format statement: which includes information on the type of data present in the file and some of its attributes. The Format statement should be generally written after the Title or the Description statement. All taxa names must be written according to a set of rules.
  • contains one or more command statements
  • A command statement contains a command and a valid setting keyword (command=keyword format

• Comments: can be written anywhere in the data file and can span multiple lines. They must always be enclosed in square brackets ([and]) brackets and can be nested.
• keywords: can be written in any combination of lower- and upper-case letters
• Rules for Taxa Names: Distance matrices as well as sequence data may come from species, populations, or individuals. These evolutionary entities are designated as OTUs (Operational Taxonomic Units) or taxa. Each taxon must have an identification tag, i.e., a taxon Iabel according to the following conventions:
  • ‘#’ Sign: Every Iabel must be written on a new line, and a '#' sign must precede the label. There are no restrictions on the length of the Iabels in the data file. The labels are not required to be unique, although identical labels may result in ambiguities and should be avoided.
  • Characters: Taxa labels must start with alphanumeric characters (0-9, a-z, and A-Z) or a special character: -, + or .. 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.

• When referring to MEGA in the main text of your publication, you may choose a format such as:
  

Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 4 (Tamura, Dudley, Nei, and Kumar 2007).

• 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)