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
