MEGA: Requirements and capabilities

IMEG at psuvm.psu.edu IMEG at psuvm.psu.edu
Tue Aug 31 11:53:35 EST 1993

MEGA (Molecular Evolutionary Genetics Analysis)
Version 1.0

(c) Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei
    and Pennsylvania State University

--------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).

-------Functions in MEGA-------


   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

      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

      Variable sites
      Parsimony-informative sites
      Two-fold redundant sites
      Four-fold redundant sites

      Translation of nucleotide sequences into amino acid sequences

      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
         Number of nucleotide differences
         Nucleotide substitutions
         Transitional substitutions
         Transversional substitutions
         Transition/transversion ratio
      Distance measures:
         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:
         Mammalian mitochondrial
         Drosophila mitochondrial
         Yeast mitochondrial
         Synonymous substitutions
         Nonsynonymous substitutions
         Average distances for all pairwise comparisons
         and standard errors

   Amino acid substitutions
      Distance measurers:
         Number of amino acid differences
         Poisson-correction distance
         Gamma distance

   Distance output:
      Control on:
         Page size
         Precision for distance output
         Distance q standard error formats

Tree building and test

      Neighbor-joining (NJ)
      Maximum parsimony (MP):
         Branch-and-bound search
         Heuristic search

   Statistical Tests:
      Bootstrap test:
      Branch length test:

   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

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