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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 ouput 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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