dawg(1) DNA assembly with gaps, a DNA sequence simulator

DESCRIPTION

dawg 1.2-release DNA Assembly With Gaps Copyright © 2004-2009 Reed A. Cartwright

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.*

LICENSE

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.

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.

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

Send Bug Reports to [email protected]