dawg -[scubvhqew?] [-o outputfile] file1 [file2...]  
  -s: process files serially [default]
  -c: process files combined together
  -u: unbuffered output
  -b: buffered output [default]
  -q: disable error and warning reports (quiet)
  -e: enable error reports [default]
  -w: enable warning reports [default]
  -v: display version information
  -h: display help information
  -?: same as -h
  -o outputfile: override output filename in the configuration file

  Dawg will read stdin if filename is "-".

FILE FORMAT
  The file format takes a series of statements in the form of
  "name = value," where "name" is alphanumeric and value can be a string,
  number, boolean, tree, or vector of values.  A single variable is
  equivalent to a vector of a single entry.

string:  "[char-sequence]"
         '[char-sequence]'
         """[multi-line char-sequence]""" (rm initial and final newlines)
         '''[multi-line char-sequence]''' (kp initial and final newlines)
number:  [sign]digits[.digits][(e|E)[sign]digits]
boolean: true|false
tree:    Newick Format
vector:  { value, value, ...}

OPTIONS

  Name            Type            Description
--------------------------------------------------------------------------
  Tree             VT  phylogeny
  TreeScale        N   coefficient to scale branch lengths by
  Sequence         VS  root sequences 
  Length           VN  length of generated root sequences
  Rates            VVN rate of evolution of each root nucleotide
  Model            S   model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN
  Freqs            VN  nucleotide (ACGT) frequencies 
  Params           VN  parameters for the model of evolution
  Width            N   block width for indels and recombination
  Scale            VN  block position scales
  Gamma            VN  coefficients of variance for rate heterogenity
  Alpha            VN  shape parameters
  Iota             VN  proportions of invariant sites
  GapModel         VS  models of indel formation: NB|PL|US
  Lambda           VN  rates of indel formation
  GapParams        VVN parameter for the indel model
  Reps             N   number of data sets to output
  File             S   output file 
  Format           S   output format: Fasta|Nexus|Phylip|Clustal
  GapSingleChar    B   output gaps as a single character
  GapPlus          B   distinguish insertions from deletions in alignment
  KeepFlank        N   undeletable flanking regions N nucs from sequence
  KeepEmpty        B   preserve empty columns in final alignment
  LowerCase        B   output sequences in lowercase
  Translate        B   translate outputed sequences to amino acids
  Seed             VN  pseudo-random-number-generator seed (integers)
  Out.Block.Head   S   string to insert at the start of the output
  Out.Block.Tail   S   string to insert at the end of the output
  Out.Block.Before S   string to insert before a sequence set in the output
  Out.Block.After  S   string to insert after a sequence set in the output
  Out.Subst        B   do variable subsitution in Out.Block.*
  
