MEGA: Mol. Evol. Gen. Analysis Program
IMEG at psuvm.psu.edu
Wed Feb 2 09:07:20 EST 1994
This document contains many pages, including
1. Cover letter
2. Order form (We no longer accept purchase orders)
3. Hardware and software requirements
4. Program upgrade policy
5. Functions in MEGA
MEGA version 1.0, 1.01
To whom it may concern:
A computer software called MEGA: Molecular Evolutionary
Genetics Analysis has been developed. This software is for
facilitating statistical studies of molecular evolution by
using IBM compatible personal computers. It contains
various methods of estimating evolutionary distances and
three different methods of phylogenetic inference (UPGMA,
neighbor-joining, and maximum parsimony) with either a
standard-error test or a bootstrap test of topological
differences. For the maximum parsimony method, new
algorithms of the branch-and-bound and heuristic searches
are implemented. MEGA also computes basic statistical
quantities such as nucleotide and amino acid frequencies,
transition/transversion bias, codon usage frequencies,
number of variable sites, etc. In addition, advance on-
screen sequence data and phylogenetic tree editors are
included. Integrated and interactive designs, on-line
context-sensitive helps, text-file editor, and other unique
features make it easy to use MEGA.
MEGA version 1.0 is distributed with a nominal fee to
defray the cost of producing the user manual (140 pp.) and diskettes,
and the mailing and handling expenses (see enclosed order form).
However, for anyone who is unable to pay the fee for some
reason, it will be provided free of charge after receiving a
letter explaining the circumstances. MEGA will not be sent
by electronic-mail because the accompanying manual cannot be
included in this case.
Technical questions and other inquires about MEGA
should be directed to the senior author of the software.
Please include your electronic-mail address, if any.
Telephone: (814) 863-7334
FAX: (814) 863-7336
E-mail: imeg at psuvm,
imeg at psuvm.psu.edu
MEGA ORDER FORM
Program No Charge
User manual, diskette, shipping, and handling $ 15.00
For shipment outside North America add $10.00 _________
(We will use first class airmail)
* This cost can be waived if the circumstances for the inability to
pay (e.g., lack of hard currencies in some countries) are explained.
Diskette type desired: Please specify:
[ ] 3.5" Diskette (1.44MB) [ ] DOS Version ......
[ ] 5.25" Diskette (1.2MB) [ ] Computer system...
[ ] other (specify).... [ ] Do you use windows? Yes/No
All orders must be prepaid in U.S. dollars. Return this form together
with a check or money order payable to Penn State University at the
following address. Purchase orders will not be accepted.
Institute of Molecular Evolutionary Genetics
The Pennsylvania State University
328 Mueller Laboratory
University Park, PA 16802 USA
E-mail: IMEG at PSUVM.PSU.edu, IMEG at PSUVM
About the user:
Telephone: _____________________ Fax: _________________
--------Hardware and Software------
IBM and IBM-compatible PCs, XTs, ATs, etc.
640KB RAM memory.
DOS version 3.3 or later.
Hard disk with 2MB free.
No extended or expanded memory required.
No graphics adapters required.
No math-chip required.
Supports the keyboard as well as the mouse (not essential).
------- Program upgrade policy ----
Since MEGA is in its first version, there may be many software
bugs in the program. We are considering to provide registered users
a version where bugs reported in version 1.0 and 1.01 will be fixed. As you
may notice from the order form, we are just trying to recover the
cost of distributing MEGA only. So we are not in a position to
provide many upgrades. In any case, we do not plan to include new
methods in MEGA soon (for at least one year), and therefore the
questions about upgrades may not be so pressing at this moment.
-------Functions in MEGA-------
Amino acid sequences
Upper-triangular distance matrix
Lower-triangular distance matrix
Alignment gap symbol
Missing-information site symbol
Identical site symbol
In-memory data editing features
Domains of sequences
Individual sites and codons
Exclude/include missing information sites
Exclude/include alignment gap sites
Edit OTU labels
Restore OTU labels
Sequence data presentation
Two-fold redundant sites
Four-fold redundant sites
Translation of nucleotide sequences into amino acid sequences
Only variable sites
Only parsimony-informative sites
Amino acid sequences translated
Nucleotide and amino acid frequencies
Nucleotide pair frequencies in pairwise comparisons
Codon usage frequencies
Relative synonymous codon usage (RSCU) values
Variable sites in overlapping segments
Variable sites in nonoverlapping segments
Number of nucleotide differences
Kimura 2-parameter distance
Kimura 2-parameter model
Genetic code tables:
Average distances for all pairwise comparisons
and standard errors
Amino acid substitutions
Number of amino acid differences
Precision for distance output
Distance q standard error formats
Tree building and test
Maximum parsimony (MP):
Branch length test:
Swapping and flipping branches
Multiple page printouts
Choice of fonts
Choice of orientation
Choice of page size
Exiting to DOS temporarily
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