DAWG VERSION 1.0.0 - DNA ASSEMBLY WITH GAPS

Copyright (C) (2005) Reed A. Cartwright - All rights reserved.

DESCRIPTION

Dawg is an application that will simulate nucleotide evolution with gaps.

CONTACT

rac@uga.edu or reed@scit.us

LICENSE

See COPYING for license information.

INSTALLATION

See INSTALL for installation instructions.

DOWNLOAD

Dawg 1.0.0 can be downloaded from <http://www.genetics.uga.edu/sw/>, all
later versions can be downloaded from the development page for Dawg,
<http://scit.us/dawg/>.

MAILING LIST

To participate in the development of Dawg you can subscribe to the mailing
list at <http://scit.us/mailman/listinfo/dawg>.  

EXAMPLES
  example0.dawg - minimal
  example1.dawg - typical usage
  example2.dawg - simple indel formation
  example3.dawg - robust indel formation
  example4.dawg - recombination 

COMMAND LINE USAGE
  dawg -[scubvh?] file1 [file2...]
  -s: process files serially [default]
  -c: process files combined together
  -u: unbuffered output
  -b: buffered output [default]
  -v: display version information
  -h: display help information
  -?: same as -h

  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]"
           <<EOF [several lines] EOF
  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
  LowerCase      B   output sequences in lowercase
  Translate      B   translate outputed sequences to amino acids
  NexusCode      S   text or file to include between datasets in Nexus format
  Seed           VN  PRNG seed (integers)

DEFAULTS

  TreeScale = 1.0
  Length = 100
  Model = "JC"
  Freqs = {0.25,0.25,0.25,0.25}
  Params = {1.0,1.0,1.0,1.0,1.0,1.0}
  Width = 1
  Scale = 1.0
  Gamma = 0.0
  Iota =  0.0
  GapModel = "US"
  GapParams = 1.0
  Reps = 1
  Format = "Fasta"
  GapSingleChar = false
  GapPlus = false
  LowerCase = false
  Translate = false

NOTES

The meaning of the "Params" vector is different for each substitution model.
  GTR: Substitution rates A-C, A-G, A-T, C-G, C-T, G-T
  JC:  Ignored
  K2P: Transition rate, Transversion rate
  K3P: Alpha (Transitions), Beta (A-T & G-C), Gamma (A-C & G-T)
  HKY: Transition rate, Transversion rate
  F81: Ignored
  F84: Kappa
  TN:  Alpha1 (A-G), Alpha2 (C-T), Beta (Transversions)

Parameter "Freqs" is ignored by the models "JC", "K2P", and "K3P".

If "Lambda" is a single value, then it specifies the rate of indel formation, e.g.
"Lambda = 0.1" is the same as "Lambda = {0.05, 0.05}".  The first parameter is the
insertion rate and the second parameter is the deletion rate.

The first parameter of "GapModel" specifies the distribution model of insertion sizes.
The second parameter specifies the distribution model of deletion sizes.  If only one
parameter is given it is the model for both insertions and deletions.

The first parameter of "GapParams" is a vector specifying the parameters for the
gap model of insertions.  Likewise the second parameter is a vector specifying the
parameters for the gap model of deletions.  If "GapParams" is not a vector of vectors,
then it specifies the vector of parameters for both insertions and deletions.

The meaning of the GapParams vector is different for each gap model.
  US: The distribution of gap sizes.
  NB: The number of failures (r), the probability of success (q).
  PL: The rate parameter (a), the maximum gap size.

To create a recombinant tree, you may need to specifically describe and label the
inner nodes at which the recombination events occur.  See example4.dawg.

Gamma takes precidence over Alpha.

Sequence takes precidence over Length.

If NexusCode is the name of a file, the code is read from that file.

The following vector parameters have a size of "Width": "Scale", "Alpha", "Gamma",
and "Iota".  If their size is less than width then the first value in the vector
will be used to fill in the rest of the values, e.g. "Scale = 1.0" is the same as
"Scale = {1.0,1.0,1.0}" when "Width = 3".