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, imeg@psuvm.psu.edu 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: IMEG@PSUVM.PSU.edu, 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