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

   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



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