Subject: MEGA



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

                                                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@psuvm,
                                          [email-masked]

                    MEGA ORDER FORM

Cost*
-----------------------------------------------------------------
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                                                   _________
-----------------------------------------------------------------
* 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.

     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:     [email-masked], IMEG@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