.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH DAWG "1" "December 2015" "dawg 1.2-release" "User Commands"
.SH NAME
dawg \- DNA assembly with gaps, a DNA sequence simulator
.SH DESCRIPTION
dawg 1.2\-release
DNA Assembly With Gaps
Copyright \(co 2004\-2009 Reed A. Cartwright
.PP
dawg \fB\-[scubvhqew\fR?] [\-o outputfile] file1 [file2...]
.HP
\fB\-s\fR: process files serially [default]
.HP
\fB\-c\fR: process files combined together
.HP
\fB\-u\fR: unbuffered output
.HP
\fB\-b\fR: buffered output [default]
.HP
\fB\-q\fR: disable error and warning reports (quiet)
.HP
\fB\-e\fR: enable error reports [default]
.HP
\fB\-w\fR: enable warning reports [default]
.HP
\fB\-v\fR: display version information
.HP
\fB\-h\fR: display help information
.HP
\-?: same as \fB\-h\fR
.HP
\fB\-o\fR outputfile: override output filename in the configuration file
.IP
Dawg will read stdin if filename is "\-".
.PP
FILE FORMAT
.IP
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.
.PP
string:  "[char\-sequence]"
.IP
\&'[char\-sequence]'
"""[multi\-line char\-sequence]""" (rm initial and final newlines)
\&'''[multi\-line char\-sequence]''' (kp initial and final newlines)
.PP
number:  [sign]digits[.digits][(e|E)[sign]digits]
boolean: true|false
tree:    Newick Format
vector:  { value, value, ...}
.PP
OPTIONS
.TP
Name
Type            Description
.PP
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
.TP
Tree
VT  phylogeny
.TP
TreeScale
N   coefficient to scale branch lengths by
.TP
Sequence
VS  root sequences
.TP
Length
VN  length of generated root sequences
.TP
Rates
VVN rate of evolution of each root nucleotide
.TP
Model
S   model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN
.TP
Freqs
VN  nucleotide (ACGT) frequencies
.TP
Params
VN  parameters for the model of evolution
.TP
Width
N   block width for indels and recombination
.TP
Scale
VN  block position scales
.TP
Gamma
VN  coefficients of variance for rate heterogenity
.TP
Alpha
VN  shape parameters
.TP
Iota
VN  proportions of invariant sites
.TP
GapModel
VS  models of indel formation: NB|PL|US
.TP
Lambda
VN  rates of indel formation
.TP
GapParams
VVN parameter for the indel model
.TP
Reps
N   number of data sets to output
.TP
File
S   output file
.TP
Format
S   output format: Fasta|Nexus|Phylip|Clustal
.TP
GapSingleChar
B   output gaps as a single character
.TP
GapPlus
B   distinguish insertions from deletions in alignment
.TP
KeepFlank
N   undeletable flanking regions N nucs from sequence
.TP
KeepEmpty
B   preserve empty columns in final alignment
.TP
LowerCase
B   output sequences in lowercase
.TP
Translate
B   translate outputed sequences to amino acids
.TP
Seed
VN  pseudo\-random\-number\-generator seed (integers)
.TP
Out.Block.Head
S   string to insert at the start of the output
.TP
Out.Block.Tail
S   string to insert at the end of the output
.TP
Out.Block.Before S
string to insert before a sequence set in the output
.TP
Out.Block.After
S   string to insert after a sequence set in the output
.TP
Out.Subst
B   do variable subsitution in Out.Block.*
.PP
.SH "LICENSE"
.PP
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.PP
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
.PP
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111\-1307  USA
.PP
Send Bug Reports to reed@scit.us.