Molecular Evolutionary Genetics Analysis
Version 1.01
Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei
Institute ofMolecular Evolutionary Genetics
The Pennsylvania State University
University Park, PA 16802
US A
�GA is distributed with a nominal fee to defray the cost of producing the user manual, the
diskette(s), and the mailing and handling expenses (see order form). However, for anyone who
is unable to pay the fee for some reason (e.g., lack of hard currencies in some countries), it will
be provided free of charge after receiving a letter of explanation. MEGA will not be sent by
electronic-mail because the accompanying manual cannot be included in this case. To obtain an
order form, contact Joyce White or the authors at the address given below.
Although utmost care has been taken to ensure the correctness of the software, the
software is provided "as is" without any warranty of any kind. In no event shall the
authors and their employers be liable for any damages, including but not limited to
special, consequential, or other damages. Authors specifically disclaim all other
warranties, expressed or implied, including but not limited to the determination of
suitability of this product for a specific purpose, use, or application.
Copyright (c) 1993 Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei
and
The Pennsylvania State University
All rights reserved
Suggested Citation:
Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei. 1993. MEGA: Molecular
Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State
University, University Park, PA 16802.
Distribution:
Institute of Molecular Evolutionary Genetics
328 Mueller Laboratory
The Pennsylvania State University
University Park, PA 16802, USA
Telephone:
Fax:
E-mail:
814-863-7334 (not for technical assistance)
814-863-7336
imeg@psuvm.psu.edu
imeg@psuvm
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l�put file formats for different kinds of data are discussed in this chapter. In
addition, the use of in-memory data editing options is explained. Note that there is no
limit on the amount of molecular sequence or distance matrix data that can be analyzed
in MEGA; the size of data set is constrained only by the computer memory available.
2.1 MEGA Format
Either sequence data or distance data can be entered in MEGA as ASCII-text
files. These data must be organized in a format specific to MEGA. These input file
for1nats are consistent and flexible, and they include options for writing extensive
comments in the data file.
2.1.1 Key Words
Every data file must contain the key words #MEGA and TITLE. These key
words can be written in any combination of lower- and upper-case letters.
#MEGA
This key word indicates that the data file is prepared for analysis using
MEGA. It must be present on the very first line in the data file.
TITLE
The word TITLE must be written on the second line. It may be followed
by some description of data on the same line. This description is written in
all the output files containing results. If the specified description exceeds
128 characters in length, the additional characters are ignored.
After the MEGA format identifier (#MEGA) and the title (fll1LE), the data
should follow. Comments may be written on one or more lines right after the TI'l'LE
line and before the data (see examples in sections 2.2 and 2.3).