Mercurial > repos > abims-sbr > concatphyl

annotate ConcatPhyl.xml @ 0:6d930f037fea draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
author abims-sbr
date Thu, 13 Apr 2017 05:49:32 -0400
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children 1f8d039bd241
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1 <tool name="ConcatPhyl" id="concatphyl" version="1.0">
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3 <description>
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4 Concatenation and phylogeny
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5 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <requirements>
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12 <expand macro="python_required" />
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13 <!-- <requirement type="package" version="1.3.1">samtools</requirement> -->
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14 <requirement type="package" version="8.2.9">raxml</requirement>
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15 </requirements>
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17 <command><![CDATA[
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18 python $__tool_directory__/scripts/S01_concatenate.py ${zip}
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20 #if $format.format_run == "nucleic" :
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21 nucleic $format.zip_nuc
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22 #elif $format.format_run == "proteic" :
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23 proteic $format.zip_aa
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24 #end if
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25 > ${output};
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27 raxmlHPC
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28 #if $format.format_run == "nucleic" :
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29 -n "galaxy_run"
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30 ##-q "./05_partitions_gene_NUC"
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31 -s "./03_Concatenation_nuc.phy"
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32 ## (-m)
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33 -m $format.base_model
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34 #elif $format.format_run == "proteic" :
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35 -n "galaxy_run"
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36 ##-q "./06_partitions_gene_AA"
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37 -s "./02_Concatenation_aa.phy"
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38 ## (-m)
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39 -m $format.base_model$format.aa_search_matrix
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40 #end if
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42 ## --- Optional parameters ---
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44 ##if $raxml_options.options == "yes" :
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46 ## (-p)
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47 #if $random_seed:
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48 -p $random_seed
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49 #else
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50 -p 1234567890
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51 #end if
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53 ## (-N/#)
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54 #if $number_of_runs:
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55 -N $number_of_runs
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56 #end if
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57 #if $number_of_runs_bootstop:
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58 -# $number_of_runs_bootstop
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59 #end if
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60
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61 ## (-f)
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62 #if $search_algorithm:
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63 -f $search_algorithm
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64 #end if
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65
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66 ## (-x)
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67 #if $rapid_bootstrap_random_seed:
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68 -x $rapid_bootstrap_random_seed
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69 #end if
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70 ##else :
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72 ##-N 100 -f a -x 12345
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73
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74 ##end if
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75 >> ${output};
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76 ]]>
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77 </command>
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78
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79 <inputs>
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80
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81 <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" />
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82 <conditional name="format">
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83 <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">
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84 <option value="nucleic">Nucleic format</option>
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85 <option value="proteic">Proteic format</option>
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86 </param>
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87
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88 <when value="nucleic">
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89 <param name="zip_nuc" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="It must contain the aligned files without indels in NUCLEIC format" />
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90 <!-- ## Nucleotide substitution models -->
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91 <param name="base_model" type="select" label="Substitution Model">
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92 <option value="GTRCAT">GTRCAT</option>
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93 <option value="GTRCATI">GTRCATI</option>
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94 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
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95 <option value="GTRGAMMAI">GTRGAMMAI</option>
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96 </param>
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97 </when>
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98
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99 <when value="proteic">
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100 <param name="zip_aa" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="It must contain the aligned files without indels in PROTEIC format" />
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101 <!-- ## Aminoacid substitution models -->
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102 <!--<param name="aa_model_empirical_base_frequencies" type="boolean" checked="no" truevalue="F" falsevalue="X" display="checkboxes" label="Use empirical base frequencies in AA models." /> -->
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103 <param name="base_model" type="select" label="Substitution Model (-m)">
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104 <option value="PROTCAT" selected="true">PROTCAT</option>
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105 <option value="PROTCATI">PROTCATI</option>
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106 <option value="PROTGAMMA">PROTGAMMA</option>
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107 <option value="PROTGAMMAI">PROTGAMMAI</option>
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108 </param>
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109 <param name="aa_search_matrix" type="select" label="Matrix">
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110 <option value="DAYHOFF" selected="true">DAYHOFF</option>
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111 <option value="JTT">JTT</option>
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112 <option value="WAG">WAG</option>
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113 <option value="BLOSUM62">BLOSUM62</option>
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114 </param>
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115 </when>
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116 </conditional>
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117
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118 <!-- <conditional name="raxml_options"> -->
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119
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120 <!--
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121 <param name="options" type="select" label="Raxml advanced options">
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122 <option value="yes">Yes</option>
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123 <option value="no" select="true">No</option>
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124 </param>
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125
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126 -->
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127
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128 <!-- <when value="yes"> -->
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129
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130 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random seed used for the parsimony inferences" />
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131
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132 <!-- ## (-N/#) -->
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133 <param name="number_of_runs" type="integer" size="8" value="100"
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134 label="Number of runs" help="Specify the number of
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135 alternative runs (-N|#) on distinct starting trees In combination
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136 with the '-b' option will invoke a multiple boostrap analysis.
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137 You can add the bootstopping criteria by choosing the autoMR,
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138 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
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139 providing a number here. Bootstopping will only work in
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140 combination with '-x' or '-b'."
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141 optional="True" />
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142 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
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143 <option value="" selected="yes"></option>
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144 <option value="autoMR">autoMR</option>
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145 <option value="autoMRE">autoMRE</option>
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146 <option value="autoMRE_IGN">autoMRE_IGN</option>
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147 <option value="autoFC">autoFC</option>
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148 </param>
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149
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150 <!-- ## (-f) -->
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151 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
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152 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
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153 <option value="A">Compute marginal ancestral states (A)</option>
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154 <option value="b">Draw bipartition information (b)</option>
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155 <option value="c">Check if the alignment can be read (c)</option>
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156 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
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157 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
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158 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
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159 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
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160 <option value="j">Generate bootstrapped alignment files (j)</option>
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161 <option value="J">Compute SH-like support values for the -t tree (J)</option>
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162 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
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163 <option value="n">Compute log likelihood score for -z trees (n)</option>
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164 <option value="o">Use old slower search algorithm (o)</option>
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165 <option value="p">Stepwise MP addition of new sequences (p)</option>
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166 <option value="q">Fast quartet calculator (q)</option>
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167 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
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168 <option value="s">Split a multi-gene alignment (s)</option>
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169 <option value="S">Compute site-specific placement bias (S)</option>
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170 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
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171 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
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172 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
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173 <option value="v">Classify environmental sequences (v)</option>
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174 <option value="w">Compute ELW-test on -z trees (w)</option>
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175 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
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176 <option value="y">Classify environmental sequences into a reference tree (y)</option>
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177 </param>
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178
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179 <!-- ## (-q) -->
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180 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." />
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181
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182 <!-- ## (-x) -->
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183 <param name="rapid_bootstrap_random_seed" type="integer" value='1234567890' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
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184 <!-- </when> -->
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185
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186
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187 <!-- </conditional> -->
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188
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189 <param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? ">
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190 <option value="nothing">No output</option>
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191 <option value="fasta">Fasta format</option>
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192 <option value="phylip">Phylip format</option>
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193 <option value="nexus">Nexus format</option>
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194 </param>
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195 <!-- -m GTRGAMMA -N 100 -f a -x 12345 -->
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196
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197 <param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " />
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198 <param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " />
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199 <param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/>
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200
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201 </inputs>
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202
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203 <outputs>
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204 <data name="output" format="txt" label="Phylogeny"/>
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205
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206 <data name="out_fasta_aa" format="fasta" label="Phylogeny_concatenation_fasta_aa" from_work_dir="02_Concatenation_aa.fas">
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207 <filter>format['format_run'] == "proteic" and out == "fasta"</filter>
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208 </data>
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209
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210 <data name="out_phylip_aa" format="phylip" label="Phylogeny_concatenation_phylip_aa" from_work_dir="02_Concatenation_aa.phy">
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211 <filter>format['format_run'] == "proteic" and out == "phylip"</filter>
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212 </data>
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213
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214 <data name="out_nexus_aa" format="nexus" label="Phylogeny_concatenation_nexus_aa" from_work_dir="02_Concatenation_aa.nex">
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215 <filter>format['format_run'] == "proteic" and out == "nexus"</filter>
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216 </data>
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217
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218 <data name="out_fasta_nuc" format="fasta" label="Phylogeny_concatenation_fasta_nuc" from_work_dir="03_Concatenation_nuc.fas">
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219 <filter>format['format_run'] == "nucleic" and out == "fasta"</filter>
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220 </data>
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221
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222 <data name="out_phylip_nuc" format="phylip" label="Phylogeny_concatenation_phylip_nuc" from_work_dir="03_Concatenation_nuc.phy">
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223 <filter>format['format_run'] == "nucleic" and out == "phylip"</filter>
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224 </data>
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225
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226 <data name="out_nexus_nuc" format="nexus" label="Phylogeny_concatenation_nexus_nuc" from_work_dir="03_Concatenation_nuc.nex">
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227 <filter>format['format_run'] == "nucleic" and out == "nexus"</filter>
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228 </data>
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229
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230 <data name="out_raxml1" format="txt" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run">
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231 <filter>raxml1 == True</filter>
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232 </data>
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233
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234 <data name="out_raxml3" format="txt" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run">
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235 <filter>raxml3 == True</filter>
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236 </data>
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237
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238 <data name="out_raxml4" format="txt" label="Phylogeny_RAxML_BootStrap" from_work_dir="RAxML_bootstrap.galaxy_run">
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239 <filter>raxml4 == True</filter>
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240 </data>
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241 </outputs>
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242
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243 <tests>
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244 <test>
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245 <param name="zip" ftype="zip" value="from_filter_oase.zip" />
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246 <conditional name="format">
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247 <param name="format_run" value="nucleic" />
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248 <param name="zip_nuc" ftype="zip" value="test_05_output_CDS_Search_input_ConcatPhyl.zip" />
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249 <param name="base_model" value="GTRGAMMA" />
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250 </conditional>
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251 <param name="random_seed" value="1234567890" />
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252 <param name="number_of_runs" value="100" />
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253 <param name="number_of_runs_bootstop" value="" />
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254 <param name="search_algorithm" value="d" />
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255 <!-- <param name="multiple_model" value="" /> -->
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256 <param name="rapid_bootstrap_random_seed" value="123456789" />
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257 <param name="out" value="nothing" />
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258 <param name="raxml1" value="True" />
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259 <param name="raxml3" value="True" />
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260 <param name="raxml4" value="True" />
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261 <output name="out_raxml4">
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262 <assert_contents>
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263 <has_text text="(Ap,(((Pf,Ph),Pg),((Pu,Te),(Am,Th))),Ac);"/>
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264 <has_text text="(Ap,(Ph,(Pg,((Pf,(Pu,Te)),(Am,Th)))),Ac);"/>
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265 <has_text text="(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac);"/>
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266 </assert_contents>
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267 </output>
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268
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269 </test>
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270 </tests>
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271
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272 <help>
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273
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274 ============
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275 What it does
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276 ============
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277
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278 | This tool takes a zip file containing nucleic fasta sequence files and searches different homologous genes from pairwise comparisons.
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279 |
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280 |
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281 | The run RAxML was written by **Alexandros Stamatakis**.
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282 | The script was written by **Eric Fontanillas**.
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283 | The wrapper was written by **Julie Baffard**.
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284
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285 --------
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286
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287 ==========
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288 Parameters
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289 ==========
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290
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291 | The choice of the format sequences is possible : **proteic** or **nucleic**
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292 |
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293
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294 The choice of parameters for the RAxML run is possible :
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295
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296 **-m** :
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297 | is the option for the choice of the substitution model.
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298 | By default it's GTRGAMMA.
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299 |
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300
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301 **-N** :
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302 | is the option for the choice of the number of run
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303 | by default it's 100
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304 |
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305
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306 **rapid bootstrapping** :
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307 | is the option to have, in addition to the best tree search, the rapid bootstrapping
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308 | this translates by : -x 12345 -f a
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309 | by default, this option is choosen
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310 |
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311
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312 --------
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313
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314 ======
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315 Inputs
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316 ======
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317
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318 option **Select a zip file containing the input files** :
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319
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320 | the input zip file must have the extension .ort.zip
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321 | At the beginning, when you upload your input, you have to change the extension .zip to .ort.zip
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322
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323
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324 --------
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325
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326 =======
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327 Outputs
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328 =======
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329
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330 This tool, produces the following files :
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331
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332 **Phylogeny** :
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333 | is the general output. It gives the information about the concatenation (statistics) and the RAxML run.
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334 |
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335
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336 **Phylogeny_concatenation_fasta_aa** :
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337 | is the output which contains the sequences concatenated in fasta format when you choose the option proteic
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338 |
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339
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340 **Phylogeny_concatenation_phylip_aa** :
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341 | is the output which contains the sequences concatenated in phylip format when you choose the option proteic
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342 |
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343
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344 **Phylogeny_concatenation_nexus_aa** :
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345 | is the output which contains the sequences concatenated in nexus format when you choose the option proteic
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346 |
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347
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348 **Phylogeny_concatenation_fasta_nuc** :
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349 | is the output which contains the sequences concatenated in fasta format when you choose the option nucleic
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350 |
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351
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352 **Phylogeny_concatenation_phylip_nuc** :
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353 | is the output which contains the sequences concatenated in phylip format when you choose the option nucleic
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354 | it's this output which is used for the RAxML run
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355 |
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356
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357 **Phylogeny_concatenation_nexus_nuc** :
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358 | is the output which contains the sequences concatenated in nexus format when you choose the option nucleic
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359 |
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360
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361 **Phylogeny_RAxML_BestTree** :
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362 | is the output of RAxML run which contains the Best Tree found
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363 |
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364
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365 **Phylogeny_RAxML_BiPartitionBranchLabel** :
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366 | is the output of RAxML run which contains the Best Tree found with supported values as branch labels
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367 |
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368
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369 **Phylogeny_RAxML_BiPartition** :
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370 | is the output of RAxML run which contains the Best Tree found with supported values
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371 |
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372
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373 **Phylogeny_RAxML_BootStrap** :
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374 | is the output of RAxML run which contains all the boostrapped trees
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375 | the number of boostraped trees depending of the option -N (number of run)
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376 |
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377
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378 --------
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379
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380 ===============
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381 Working Example
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382 ===============
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383
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384 ---------------------------
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385 The input files and options
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386 ---------------------------
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387
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388 **Input files**
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389 | 6 files with 200 nucleic sequences each
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390 | a zip file containing 2 locus aligned without indel (in nucleic format)
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391 |
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392 **Parameters**
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393 | option : nucleic
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394 | no option for the RAxML run, so by default it's : -m GTRGAMMA -N 100 -f a -x 12345
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395 |
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396
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397 ----------------
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398 The output files
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399 ----------------
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400
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401 **Phylogeny** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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402
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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403 | ******************** CONCATENATION ********************
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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404 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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405 | Process nucleotides concatenation:
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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406 | Number of taxa aligned = 6
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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407 | Number of loci concatenated = 2
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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408 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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409 | Total length of the concatenated sequences [All codon positions] = 504
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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410 | Total length of the concatenated sequences [Codon positions 1 and 2] = 336
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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411 | Total length of the concatenated sequences [Codon position 3] = 168
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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412 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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413 |
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414 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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415 | ******************** RAxML RUN ********************
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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416 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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417
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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418 the informations of the RAxML run
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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419
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420 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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421
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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422 **Phylogeny_concatenation_fasta_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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423
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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424 | &gt;Ps
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425
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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426 cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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427 gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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428 taccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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429
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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430 | Ac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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431
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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432 cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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433 ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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434 ------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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435
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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436 | &gt;Pp
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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437 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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438 | ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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439
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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440 | &gt;Ap
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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441
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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442 cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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443 ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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444 ccgggccttgccttccttgtctatcttgcaaagaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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445
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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446 | &gt;Pf
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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447
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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448 ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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449 cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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450 cttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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451
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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452 | &gt;Pg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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453
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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454 cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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455 tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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456 cttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
457
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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458 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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459
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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460 | If you choose the option proteic : you obtain a file with proteic sequences
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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461 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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462 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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463
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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464
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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465 **Phylogeny_concatenation_phylip_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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466
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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467 | 6 504
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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468 | Ps
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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469
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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470 cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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471 gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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472 taccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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473
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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474 | Ac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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475
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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476 cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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477 ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
478 ------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
479
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
480 | Pp
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
481 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
482 | ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
483 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
484 | Ap
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
485
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
486 cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
487 ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
488 ccgggccttgccttccttgtctatcttgcaaagaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
489
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
490 Pf
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
491 ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
492 cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
493 cttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
494
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
495 Pg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
496 cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
497 tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
498 cttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
499
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
500 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
501
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
502 | If you choose the option proteic : you obtain a file with proteic sequences
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
503 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
504 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
505
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
506 **Phylogeny_concatenation_nexus_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
507
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
508 #NEXUS
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
509
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
510 | Begin data;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
511 | Dimensions ntax=6 nchar=504;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
512 | Format datatype=dna gap=-;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
513
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
514 Matrix
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
515
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
516 Ps cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtct
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
517 ccagaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttcct
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
518 tgctttaccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
519
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
520 Ac cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
521 ggcggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
522 ------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
523
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
524 Pp ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
525 -----------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
526
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
527 Ap cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
528 ggcggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaa
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
529 ccttccgggccttgccttccttgtctatcttgcaaagaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
530
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
531 Pf ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctcc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
532 gacgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgaca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
533 accttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
534
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
535 Pg cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
536 acgtctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
537 ttgccttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
538
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
539 | ;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
540 | End;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
541 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
542
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
543 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
544
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
545 | If you choose the option proteic : you obtain a file with proteic sequences
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
546 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
547 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
548
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
549 **Phylogeny_RAxML_BestTree** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
550
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
551 | ((Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
552 | ((Pp:0.23405795780876006984,Pg:0.02012322210145659623):0.14429203507314311561,Pf:0.09977363663005259231):0.04320803212100913365,Ps:0.08351583721596630983):0.0;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
553 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
554 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
555
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
556
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
557 **Phylogeny_RAxML_BiPartitionBranchLabel** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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558
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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559 | (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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560 | (Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217[89]):0.04320803212100913365[42]):0.14429203507314311561[70],Pp:0.23405795780876006984);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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561 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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562 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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563
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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564
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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565 **Phylogeny_RAxML_BiPartition** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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566
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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567 (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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568 (Ac:0.02889451913999640381,Ap:0.01674414484251282934)89:0.17730049470177636217)42:0.04320803212100913365)70:0.14429203507314311561,Pp:0.23405795780876006984);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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569
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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570 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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571 |
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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572
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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573 **Phylogeny_RAxML_BootStrap** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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574
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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575 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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576 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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577 | (Pf,((Ap,Ac),(Pp,Pg)),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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578 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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579 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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580 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
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581 | ((Pp,Pg),(Pf,(Ap,Ac)),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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582
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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583 ...
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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584
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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585 </help>
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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586
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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587 <expand macro="citations" />
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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588
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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589 </tool>