Mercurial > repos > iuc > progressivemauve

annotate progressivemauve.xml @ 5:ce795616bd9c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
author iuc
date Sat, 27 Nov 2021 12:13:25 +0000
parents 4d869208bd52
children
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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1 <?xml version="1.0"?>
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ce795616bd9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
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2 <tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.1">
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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3 <description>constructs multiple genome alignments</description>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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4 <macros>
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5 <import>macros.xml</import>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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9 <version_command>progressiveMauve --version</version_command>
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10 <command><![CDATA[
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11 ## Symlink files in with correct extensions
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12 #for $file in $sequences:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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13 ln -s $file `basename $file`;
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14 #end for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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16 progressiveMauve
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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17 ## Input Options
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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19 #if $apply_backbone:
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20 --apply-backbone=$apply_backbone
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21 #end if
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22 --island-gap-size=$island_gap_size
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23 $mums
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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25 #if $seed_weight:
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26 --seed-weight=$seed_weight
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27 #end if
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29 #if $max_gapped_aligner_length:
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30 --max-gapped-aligner-length=$max_gapped_aligner_length
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31 #end if
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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33 #if $match_input:
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34 --match-input=$match_input
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35 #end if
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37 $collinear
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38 #if $input_guide_tree
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39 --input-guide-tree='$input_guide_tree'
ce795616bd9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
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40 #end if
0
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41 --scoring-scheme=$scoring_scheme
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42 $no_weight_scaling
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44 --max-breakpoint-distance-scale=$max_breakpoint_distance_scale
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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45 --conservation-distance-scale=$conservation_distance_scale
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46 $skip_refinement
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47 $skip_gapped_alignment
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49 #if $bp_dist_estimate_min_score:
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50 --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
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51 #end if
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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53 #if $gap_open:
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54 --gap-open=$gap_open
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55 #end if
5
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56 --repeat-penalty=$repeat_penalty
0
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57 #if $gap_extend:
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58 --gap-extend=$gap_extend
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59 #end if
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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61 #if $weight:
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62 --weight=$weight
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63 #end if
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65 #if $min_scaled_penalty:
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66 --min-scaled-penalty=$min_scaled_penalty
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67 #end if
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69 --hmm-p-go-homologous=$hmm_p_go_homologous
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70 --hmm-p-go-unrelated=$hmm_p_go_unrelated
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71 --hmm-identity=$hmm_identity
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73 $seed_family
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74 $solid_seeds
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75 $coding_seeds
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76 $no_recursion
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77 $disable_backbone
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79 ## Outputs
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80 --output=$output
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81 #if $output_guide_tree:
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82 --output-guide-tree=$output_guide_tree_file
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83 #end if
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84
5
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85 #if $backbone_output:
0
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86 --backbone-output=$output_backbone_file
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87 #end if
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88
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89 ## Sequences
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90 #for file in $sequences:
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91 `basename "${file}"`
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92 #end for
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93
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94 ]]></command>
5
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95 <inputs>
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96 <param type="data" format="fasta" name="sequences" multiple="true"
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97 label="Select sequences to align" help="in fasta format" />
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98 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="true"
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99 help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
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100
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101 <param type="integer" label="Island gap size" value="20" argument="--island-gap-size"
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102 help="Alignment gaps above this size in nucleotides are considered to be islands"/>
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103
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104 <param type="boolean" truevalue="--disable-backbone" falsevalue="" argument="--disable-backbone"
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105 label="Disable backbone" help="Disable backbone detection" />
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106
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107 <param type="boolean" truevalue="true" falsevalue="" argument="--output-guide-tree"
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108 label="Output Guide Tree" help="Write out the guide tree used for alignment to a file" />
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109
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110 <param type="boolean" truevalue="true" falsevalue="" argument="--backbone-output"
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111 label="Output Backbone" help="Write out the backbone to a file" />
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112
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113 <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" argument="--mums"
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114 help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)" />
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115
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116 <param type="integer" label="Seed weight" argument="--seed-weight" value="0" optional="true"
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117 help="Use the specified seed weight for calculating initial anchors" />
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118
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119 <param type="data" format="tabular" label="Match Input" argument="--match-input" optional="true"
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120 help="Use specified match file instead of searching for matches" />
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121
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122 <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
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123 <param type="integer" label="Max gapped aligner length" value="0" optional="true" argument="--max-gapped-aligner-length"
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124 help="Maximum number of base pairs to attempt aligning with the gapped aligner" />
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125
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126 <param type="data" format="nhx" label="input-guide-tree" optional="true" argument="--input-guide-tree"
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127 help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned" />
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128
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129 <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" argument="--collinear"
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130 help="Assume that input sequences are collinear--they have no rearrangements" />
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131
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132 <param type="select" label="Scoring scheme" argument="--scoring-scheme" help="Selects the anchoring score function" >
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133 <option value="sp" selected="true">Extant sum-of-pairs (sp)</option>
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134 <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
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135 <option value="ancestral">Ancestral (ancestral)</option>
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136 </param>
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137
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138 <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" argument="--no-weight-scaling"
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139 help="Don't scale LCB weights by conservation distance and breakpoint distance" />
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140
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141 <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" argument="--max-breakpoint-distance-scale"
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142 help="Set the maximum weight scaling by breakpoint distance" />
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143
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144 <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" argument="--conservation-distance-scale"
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145 help="Scale conservation distances by this amount" />
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146
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147 <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" argument="--skip-refinement"
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148 help="Do not perform iterative refinement" />
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149 <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" argument="--skip-gapped-alignment"
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150 help="Do not perform gapped alignment" />
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151 <param type="integer" label="BP dist estimate min score" argument="--bp-dist-estimate-min-score" value="0" optional="true"
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152 help="Minimum LCB score for estimating pairwise breakpoint distance" />
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153
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154 <param type="integer" label="Gap open" argument="--gap-open" value="0" optional="true"
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155 help="Gap open penalty" />
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156
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157 <param type="select" label="Repeat penalty" argument="--repeat-penalty"
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158 help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences">
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159 <option value="negative" selected="true">Negative</option>
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160 <option value="zero">Zero</option>
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161 </param>
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162
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163 <param type="integer" label="Gap extend" argument="--gap-extend" value="0" optional="true"
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164 help="Gap extend penalty" />
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165
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166 <!--<param type="data" label="Substitution matrix" -->
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167 <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
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168
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169 <param type="integer" label="Weight" argument="--weight" value="0" optional="true"
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170 help="Minimum pairwise LCB score" />
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171 <param type="integer" label="Min scaled penalty" argument="--min-scaled-penalty" value="0" optional="true"
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172 help="Minimum breakpoint penalty after scaling the penalty by expected divergence" />
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173
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174 <param type="float" label="HMM p go homologous" argument="--hmm-p-go-homologous" min="0" max="1" value="0.00001"
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175 help="Probability of transitioning from the unrelated to the homologous state" />
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176 <param type="float" label="HMM p go unrelated" argument="--hmm-p-go-unrelated" min="0" max="1" value="0.000000001"
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177 help="Probability of transitioning from the homologous to the unrelated state" />
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178 <param type="float" label="HMM identity" argument="--hmm-identity" min="0" max="1" value="0.7"
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179 help="Expected level of sequence identity among pairs of sequences" />
0
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180
5
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181 <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" argument="--seed-family"
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182 help="Use a family of spaced seeds to improve sensitivity" />
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183 <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" argument="--solid-seeds"
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184 help="Use solid seeds. Do not permit substitutions in anchor matches" />
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185 <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" argument="--coding-seeds"
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186 help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy" />
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187 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" argument="--no-recursion"
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188 help="Disable recursive anchor search" />
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189 </inputs>
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190 <outputs>
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191 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
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192 <change_format>
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193 <when input="mums" value="--mums" format="tabular" />
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194 </change_format>
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195 </data>
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196 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
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197 <filter>output_guide_tree and not mums</filter>
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198 </data>
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199 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
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200 <filter>backbone_output and not mums</filter>
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201 </data>
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202 </outputs>
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203 <tests>
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204 <test expect_num_outputs="1">
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205 <param name="sequences" value="phagey.fa,karma.fa" />
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206 <output name="output" file="1.xmfa" lines_diff="20" ftype="xmfa"/>
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207 </test>
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208 <test expect_num_outputs="1">
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209 <param name="sequences" value="merged.fa" />
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210 <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
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211 </test>
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212 <test expect_num_outputs="3">
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213 <param name="sequences" value="merged.fa" />
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214 <param name="output_guide_tree" value="true" />
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215 <param name="backbone_output" value="true" />
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216 <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
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217 <output name="output_guide_tree_file" file="1.nhx" />
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218 <output name="output_backbone_file" file="1.backbone" />
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219 </test>
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220 <test expect_num_outputs="1">
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221 <param name="sequences" value="merged.fa" />
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222 <param name="output_guide_tree" value="true" />
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223 <param name="mums" value="true" />
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224 <output name="output" file="1.mums" compare="sim_size" delta="1000" ftype="tabular"/>
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225 </test>
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226 <test expect_num_outputs="1">
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227 <param name="sequences" value="merged.fa" />
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228 <param name="match_input" value="1.mums" ftype="tabular"/>
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229 <output name="output" file="2.xmfa" lines_diff="24" ftype="xmfa"/>
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230 </test>
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231 </tests>
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232 <help><![CDATA[
0
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233 What it does
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234 ============
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235
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236 Mauve is a system for efficiently constructing multiple genome alignments in
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237 the presence of large-scale evolutionary events such as rearrangement and
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238 inversion. Multiple genome alignment provides a basis for research into
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239 comparative genomics and the study of evolutionary dynamics. Aligning whole
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240 genomes is a fundamentally different problem than aligning short sequences.
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241
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242 Mauve has been developed with the idea that a multiple genome aligner should
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243 require only modest computational resources. It employs algorithmic techniques
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244 that scale well in the amount of sequence being aligned. For example, a pair of
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245 Y. pestis genomes can be aligned in under a minute, while a group of 9
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246 divergent Enterobacterial genomes can be aligned in a few hours.
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247
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248 progressiveMauve XMFA alignment visualized with the Mauve tool:
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249
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250 .. image:: $PATH_TO_IMAGES/hemolysin.jpg
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251
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252 Example Usage
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253 =============
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254
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255 +-----------------------------------+-------------+
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256 | Usage | Notes |
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257 +===================================+=============+
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258 | Align genomes |Simply |
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259 | |select as |
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260 | |many fasta |
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261 | |files with |
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262 | |one or more |
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263 | |sequences as |
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264 | |necessary |
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265 +-----------------------------------+-------------+
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266 | Align genomes but also save |Use the |
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267 | the guide tree and produce a |**Output |
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268 | backbone file |Guide Tree** |
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269 | |and **Output |
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270 | |Backbone** |
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271 | |options |
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272 +-----------------------------------+-------------+
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273 | Align genomes, but do not |Use the |
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274 | detect forced alignment of |**Disable |
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275 | unrelated sequences |backbone** |
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276 | |option |
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277 +-----------------------------------+-------------+
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278 | Detect forced alignment of |Use the |
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279 | unrelated sequence in the |**Apply |
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280 | alignment produced |Backbone** |
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281 | in previous example, use |option and |
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282 | custom Homology HMM transition |specify the |
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283 | parameters. |XMFA file |
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284 | |produced |
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285 | |in the |
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286 | |previous |
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287 | |example |
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288 +-----------------------------------+-------------+
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289 | Compute ungapped |Use the |
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290 | local-multiple alignments among |**MUMs** |
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291 | the input sequences |option |
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292 +-----------------------------------+-------------+
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293 | Compute an alignment of the |Set the |
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294 | same genomes, using previously |**Match |
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295 | computed local-multiple |Input** to |
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296 | alignments |the tabular |
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297 | |MUMs file |
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298 | |produced in |
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299 | |the previous |
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300 | |example |
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301 +-----------------------------------+-------------+
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302 | Set a minimum scaled |Use the |
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303 | breakpoint penalty to cope with |**Min Scaled |
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304 | the case where most genomes |Penalty** and|
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305 | are aligned correctly, but manual |set to a |
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306 | inspection reveals that |value like |
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307 | a divergent genome has too |5000 |
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308 | many predicted rearrangements. | |
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309 +-----------------------------------+-------------+
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310 | Globally align a set of |Use the |
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311 | collinear virus |**Colinear**,|
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312 | genomes, using seed families |**Seed |
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313 | to improve anchoring sensitivity |Family** |
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314 | in regions below 70% sequence |options |
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315 | identity. | |
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316 +-----------------------------------+-------------+
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317
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318
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319 The progressiveMauve algorithm: addressing limitations of the original algorithm
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320 ================================================================================
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321
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322 Comparative genomics has revealed that closely-related bacteria often have
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323 highly divergent gene content. While the original Mauve algorithm could align
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324 regions conserved among all organisms, the portion of the genome conserved
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325 among all taxa (the core genome) shrinks as more taxa are added to the
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326 analysis. As such, the original Mauve algorithm did not scale well to large
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327 numbers of taxa because it could not align regions conserved among subsets of
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328 the genomes under study. progressiveMauve employs a different algorithmic
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329 approach to scoring alignments that allows alignment of segments conserved
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330 among subsets of taxa. The progressiveMauve algorithm has been described in
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331 Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published
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332 in PLoS ONE. A brief overview is given here.
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333
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334 Finding initial local multiple alignments
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335 -----------------------------------------
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336
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337 progressiveMauve elaborates on the original algorithm for finding local
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338 multiple alignments. Instead of using a single seed pattern for match
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339 filtration, progressiveMauve uses a combination of three seed patterns for
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340 improved sensitivity. The palindromic seed patterns have been described in
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341 Darling et al. 2006 "Procrastination leads to efficient filtration for local
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342 multiple alignment"
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343
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344 Seed matches which represent a unique subsequence shared by two or more input
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345 genomes are subjected to ungapped extension until the seed pattern no longer
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346 matches. The result is an ungapped local multiple alignment with at most one
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347 component from each of the input genome sequences.
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348
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349 Computing a pairwise genome content distance matrix and guide tree
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350 ------------------------------------------------------------------
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351
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352 progressiveMauve builds up genome alignments progressively according to a guide
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353 tree. The guide tree is computed based on an estimate of the shared gene
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354 content among each pair of input genomes. For a pair of input genomes, g.x and
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355 g.y, shared gene content is estimated by counting the number of nucleotides in
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356 gx and gy aligned to each other in the initial set of local multiple
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diff changeset
357 alignments. The count is normalized to a similarity value between 0 and 1 by
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diff changeset
358 dividing by the average size of gx and gy. The similarity value is subtracted
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359 from 1 to arrive at a distance estimate. Neighbor joining is then applied to
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360 the matrix of distance estimates to yield a guide tree topology. Note that the
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361 guide tree is not intended to be a phylogeny indicative of the genealogy of
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diff changeset
362 input genomes. It is merely a computational crutch for progressive genome
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363 alignment. Also note that alignments are later refined independently of a
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364 single guide tree toplogy to avoid biasing later phylogenetic inference.
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365
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diff changeset
366 Computing a pairwise breakpoint distance matrix
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367 -----------------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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368
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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369 Prior to alignment, progressiveMauve attempts to compute a conservative
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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370 estimate of the number of rearrangement breakpoints among any pair of genomes.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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371 For each pair of genomes, pairwise alignments are created from the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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372 local-multiple alignments and the pairwise alignments are subjected to greedy
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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373 breakpoint elimination. The breakpoint penalty used for greedy breakpoint
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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374 elimination is set high for closely related genomes and scaled downward
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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375 according to the estimate of genomic content distance. Because the breakpoint
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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376 penalty is high, the resulting set of locally collinear blocks represent
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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377 robustly supported segmental homology, and a conservative estimate of the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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378 breakpoint distance can be made on this basis. The conservative estimate of
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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379 breakpoint distance is used later during progressive alignment to scale
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
380 breakpoint penalties.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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381
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
382 Progressive genome alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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383 ----------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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384
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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385 A genome alignment is progressively built up according to the guide tree. At
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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386 each step of the progressive genome alignment, alignment anchors are selected
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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387 from the initial set of local multiple alignments. Anchors are selected so that
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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388 they maximize a Sum-of-pairs scoring scheme which applies a penalty for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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389 predicting breakpoints among any pair of genomes. Because rates of genomic
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
390 rearrangement are highly variable, especially in some bacterial pathogens, some
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
391 genomes may be expected to exhibit greater rearrangement than others. As such,
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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392 a single choice of scoring penalty is unlikely to yield accurate alignments for
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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393 all genomes. To cope with this phenomenon, progressiveMauve scales the
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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394 breakpoint penalty according to the expected level of sequence divergence and
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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395 the number of well-supported genomic rearrangements among the pair of input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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396 genomes. These scaling values are taken from the distance matrices computed
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
397 earlier in the algorithm.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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398
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399 Anchored alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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400 ------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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diff changeset
401
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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402 Once anchors have been computed at a node in the guide tree, a global alignment
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
403 is computed on the basis of the anchors. Given a set of anchors among two
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
404 genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
405 global alignment algorithm is applied to compute an anchored profile-profile
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
406 alignment. MUSCLE is then used to perform tree-independent iterative refinement
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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407 on the global genome alignment.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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408
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409 Rejecting alignment of unrelated sequence
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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410 -----------------------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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411
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412 Although we compute a global alignment among sequences, genomes often contain
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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413 lineage-specific sequence and are thus not globally related. The global
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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414 alignment will often contain forced alignment of unrelated sequence. A simple
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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415 hidden Markov model structure is used to detect forced alignment of unrelated
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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416 sequence, which are then removed from the alignment.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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417
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418 Strengths of the progressiveMauve algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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419 -------------------------------------------
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420
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421 - It can be applied to a much larger number of genomes than the original Mauve
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
422 algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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423 - It can align more divergent genomes than the original algorithm. Genomes
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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424 with as little as 50% nucleotide identity can be alignable
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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425 - Manual adjustment of the alignment scoring parameters is usually not
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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426 necessary
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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427 - It aligns the pan-genome, e.g. regions conserved among subsets of the input
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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428 genomes
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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429 - It is more accurate than the previous Mauve algorithm
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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430
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parents:
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431 Notes on Reproducibility
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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432 ------------------------
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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433
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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434 The command line programme progressiveMauve seems to behave differently when::
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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435
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436 --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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437
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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438 are passed to the tool, compared to when those options are not passed. This
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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439 means that if you wish to precisely replicate the results you see in Galaxy at
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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440 the command line, you'll need to pass these flags with their "default" values.
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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441
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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442 @ATTRIBUTION@
5
ce795616bd9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
iuc
parents: 4
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443 ]]></help>
ce795616bd9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
iuc
parents: 4
diff changeset
444 <expand macro="citation" />
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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445 </tool>