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dawg - Online in the Cloud

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This is the command dawg that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


dawg - 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.*

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