| 1 | DAWG VERSION 1.0.0 - DNA ASSEMBLY WITH GAPS |
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| 2 | |
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| 3 | Copyright (C) (2005) Reed A. Cartwright - All rights reserved. |
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| 4 | |
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| 5 | DESCRIPTION |
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| 6 | |
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| 7 | Dawg is an application that will simulate nucleotide evolution with gaps. |
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| 8 | |
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| 9 | CONTACT |
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| 10 | |
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| 11 | rac@uga.edu or reed@scit.us |
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| 12 | |
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| 13 | LICENSE |
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| 14 | |
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| 15 | See COPYING for license information. |
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| 16 | |
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| 17 | INSTALLATION |
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| 18 | |
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| 19 | See INSTALL for installation instructions. |
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| 20 | |
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| 21 | DOWNLOAD |
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| 22 | |
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| 23 | Dawg 1.0.0 can be downloaded from <http://www.genetics.uga.edu/sw/>, all |
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| 24 | later versions can be downloaded from the development page for Dawg, |
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| 25 | <http://scit.us/dawg/>. |
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| 26 | |
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| 27 | MAILING LIST |
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| 28 | |
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| 29 | To participate in the development of Dawg you can subscribe to the mailing |
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| 30 | list at <http://scit.us/mailman/listinfo/dawg>. |
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| 31 | |
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| 32 | EXAMPLES |
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| 33 | example0.dawg - minimal |
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| 34 | example1.dawg - typical usage |
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| 35 | example2.dawg - simple indel formation |
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| 36 | example3.dawg - robust indel formation |
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| 37 | example4.dawg - recombination |
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| 38 | |
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| 39 | COMMAND LINE USAGE |
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| 40 | dawg -[scubvh?] file1 [file2...] |
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| 41 | -s: process files serially [default] |
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| 42 | -c: process files combined together |
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| 43 | -u: unbuffered output |
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| 44 | -b: buffered output [default] |
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| 45 | -v: display version information |
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| 46 | -h: display help information |
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| 47 | -?: same as -h |
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| 48 | |
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| 49 | Dawg will read stdin if filename is "-". |
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| 50 | |
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| 51 | FILE FORMAT |
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| 52 | The file format takes a series of statements in the form of "name = value," |
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| 53 | where "name" is alphanumeric and value can be a string, number, boolean, |
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| 54 | tree, or vector of values. A single variable is equivalent to a vector of |
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| 55 | a single entry. |
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| 56 | |
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| 57 | string: "[char-sequence]" |
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| 58 | <<EOF [several lines] EOF |
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| 59 | number: [sign]digits[.digits][(e|E)[sign]digits] |
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| 60 | boolean: true|false |
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| 61 | tree: Newick Format |
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| 62 | vector: { value, value, ...} |
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| 63 | |
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| 64 | OPTIONS |
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| 65 | Name Type Description |
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| 66 | -------------------------------------------------------------------------- |
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| 67 | Tree VT phylogeny |
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| 68 | TreeScale N coefficient to scale branch lengths by |
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| 69 | Sequence VS root sequences |
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| 70 | Length VN length of generated root sequences |
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| 71 | Rates VVN rate of evolution of each root nucleotide |
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| 72 | Model S model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN |
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| 73 | Freqs VN nucleotide (ACGT) frequencies |
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| 74 | Params VN parameters for the model of evolution |
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| 75 | Width N block width for indels and recombination |
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| 76 | Scale VN block position scales |
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| 77 | Gamma VN coefficients of variance for rate heterogenity |
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| 78 | Alpha VN shape parameters |
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| 79 | Iota VN proportions of invariant sites |
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| 80 | GapModel VS models of indel formation: NB|PL|US |
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| 81 | Lambda VN rates of indel formation |
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| 82 | GapParams VVN parameter for the indel model |
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| 83 | Reps N number of data sets to output |
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| 84 | File S output file |
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| 85 | Format S output format: Fasta|Nexus|Phylip|Clustal |
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| 86 | GapSingleChar B output gaps as a single character |
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| 87 | GapPlus B distinguish insertions from deletions in alignment |
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| 88 | LowerCase B output sequences in lowercase |
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| 89 | Translate B translate outputed sequences to amino acids |
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| 90 | NexusCode S text or file to include between datasets in Nexus format |
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| 91 | Seed VN PRNG seed (integers) |
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| 92 | |
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| 93 | DEFAULTS |
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| 94 | |
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| 95 | TreeScale = 1.0 |
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| 96 | Length = 100 |
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| 97 | Model = "JC" |
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| 98 | Freqs = {0.25,0.25,0.25,0.25} |
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| 99 | Params = {1.0,1.0,1.0,1.0,1.0,1.0} |
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| 100 | Width = 1 |
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| 101 | Scale = 1.0 |
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| 102 | Gamma = 0.0 |
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| 103 | Iota = 0.0 |
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| 104 | GapModel = "US" |
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| 105 | GapParams = 1.0 |
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| 106 | Reps = 1 |
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| 107 | Format = "Fasta" |
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| 108 | GapSingleChar = false |
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| 109 | GapPlus = false |
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| 110 | LowerCase = false |
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| 111 | Translate = false |
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| 112 | |
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| 113 | NOTES |
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| 114 | |
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| 115 | The meaning of the "Params" vector is different for each substitution model. |
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| 116 | GTR: Substitution rates A-C, A-G, A-T, C-G, C-T, G-T |
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| 117 | JC: Ignored |
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| 118 | K2P: Transition rate, Transversion rate |
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| 119 | K3P: Alpha (Transitions), Beta (A-T & G-C), Gamma (A-C & G-T) |
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| 120 | HKY: Transition rate, Transversion rate |
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| 121 | F81: Ignored |
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| 122 | F84: Kappa |
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| 123 | TN: Alpha1 (A-G), Alpha2 (C-T), Beta (Transversions) |
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| 124 | |
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| 125 | Parameter "Freqs" is ignored by the models "JC", "K2P", and "K3P". |
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| 126 | |
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| 127 | If "Lambda" is a single value, then it specifies the rate of indel formation, e.g. |
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| 128 | "Lambda = 0.1" is the same as "Lambda = {0.05, 0.05}". The first parameter is the |
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| 129 | insertion rate and the second parameter is the deletion rate. |
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| 130 | |
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| 131 | The first parameter of "GapModel" specifies the distribution model of insertion sizes. |
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| 132 | The second parameter specifies the distribution model of deletion sizes. If only one |
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| 133 | parameter is given it is the model for both insertions and deletions. |
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| 134 | |
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| 135 | The first parameter of "GapParams" is a vector specifying the parameters for the |
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| 136 | gap model of insertions. Likewise the second parameter is a vector specifying the |
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| 137 | parameters for the gap model of deletions. If "GapParams" is not a vector of vectors, |
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| 138 | then it specifies the vector of parameters for both insertions and deletions. |
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| 139 | |
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| 140 | The meaning of the GapParams vector is different for each gap model. |
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| 141 | US: The distribution of gap sizes. |
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| 142 | NB: The number of failures (r), the probability of success (q). |
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| 143 | PL: The rate parameter (a), the maximum gap size. |
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| 144 | |
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| 145 | To create a recombinant tree, you may need to specifically describe and label the |
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| 146 | inner nodes at which the recombination events occur. See example4.dawg. |
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| 147 | |
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| 148 | Gamma takes precidence over Alpha. |
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| 149 | |
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| 150 | Sequence takes precidence over Length. |
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| 151 | |
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| 152 | If NexusCode is the name of a file, the code is read from that file. |
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| 153 | |
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| 154 | The following vector parameters have a size of "Width": "Scale", "Alpha", "Gamma", |
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| 155 | and "Iota". If their size is less than width then the first value in the vector |
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| 156 | will be used to fill in the rest of the values, e.g. "Scale = 1.0" is the same as |
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| 157 | "Scale = {1.0,1.0,1.0}" when "Width = 3". |
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