This document contains many pages, including
1. Cover letter
2. Order form
3. Hardware and software requirements
4. Program upgrade policy
5. Functions in MEGA
MEGA version 1.0, 1.01
September, 1993
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.
Sincerely yours,
Sudhir Kumar
Koichiro Tamura
Masatoshi Nei
Telephone: (814) 863-7334
FAX: (814) 863-7336
E-mail: imeg at psuvm,
imeg at psuvm.psu.edu
MEGA ORDER FORM
Cost*
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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)
TOTAL _________
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* 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 are discouraged but will be accepted
if prepayment cannot be done.
Joyce White
Institute of Molecular Evolutionary Genetics
The Pennsylvania State University
328 Mueller Laboratory
University Park, PA 16802 USA
Telephone: (814)-863-7334
Fax: (814)-863-7336
E-mail: IMEG at PSUVM.PSU.edu, IMEG at PSUVM
About the user:
Name: ____________________________________________
Address: ____________________________________________
____________________________________________
____________________________________________
Telephone: _____________________ Fax: _________________
E-Mail: ____________________________________________
--------Hardware and Software------
IBM and IBM-compatible PCs, XTs, ATs, etc.
Color/monochrome monitors.
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-------
Input
Input data:
DNA sequences
RNA sequences
Amino acid sequences
Distance matrices
Input formats:
Interleaved sequences
Non-interleaved sequences
Upper-triangular distance matrix
Lower-triangular distance matrix
Choice of:
Alignment gap symbol
Missing-information site symbol
Identical site symbol
In-memory data editing features
Selection:
Desired OTUs
Domains of sequences
Individual sites and codons
Codon positions
Exclude/include missing information sites
Exclude/include alignment gap sites
Edit OTU labels
Restore OTU labels
Sequence data presentation
Highlight:
Variable sites
Parsimony-informative sites
Two-fold redundant sites
Four-fold redundant sites
Translate:
Translation of nucleotide sequences into amino acid sequences
Output:
Formats:
MEGA
PAUP
PHYLIP
Publication
Data subsets:
Only variable sites
Only parsimony-informative sites
Amino acid sequences translated
Codon positions
Sequence statistics:
Nucleotide and amino acid frequencies
Nucleotide pair frequencies in pairwise comparisons
Insertion-deletion frequencies
Codon usage frequencies
Relative synonymous codon usage (RSCU) values
Variable sites in overlapping segments
Variable sites in nonoverlapping segments
Distance estimation
Nucleotide substitutions
Quantities:
Number of nucleotide differences
Nucleotide substitutions
Transitional substitutions
Transversional substitutions
Transition/transversion ratio
Distance measures:
p-distance
Jukes-Cantor distance
Kimura 2-parameter distance
Tajima-Nei distance
Tamura distance
Tamura-Nei distance
Gamma distances
Jukes-Cantor model
Kimura 2-parameter model
Tamura-Nei model
Synonymous-nonsynonymous substitutions
Genetic code tables:
"Universal"
Mammalian mitochondrial
Drosophila mitochondrial
Yeast mitochondrial
Computation:
Synonymous substitutions
Nonsynonymous substitutions
Average distances for all pairwise comparisons
and standard errors
Amino acid substitutions
Distance measurers:
Number of amino acid differences
p-distance
Poisson-correction distance
Gamma distance
Distance output:
Control on:
Page size
Precision for distance output
Distance q standard error formats
Tree building and test
Methods:
Neighbor-joining (NJ)
UPGMA
Maximum parsimony (MP):
Branch-and-bound search
Heuristic search
Statistical Tests:
Bootstrap test:
Neighbor-joining
UPGMA
Branch length test:
Neighbor-joining
Phylogeny editing:
Tree re-rooting
Swapping and flipping branches
Consensus tree
Condensed tree
Phylogeny printing:
Various printers
Multiple page printouts
Choice of fonts
Choice of orientation
Choice of page size
Tree preview
General functions
File browsing
File editing
Exiting to DOS temporarily
Context-sensitive Helps
Error messages
