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Atelier Phylogénomique Phylogénie ARNr - Revision history
2024-03-28T18:08:45Z
Revision history for this page on the wiki
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Quentin: /* Evaluation des Alignements */
2021-10-20T13:59:42Z
<p><span class="autocomment">Evaluation des Alignements</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 13:59, 20 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for i in ~/work/ProchlorococcusSynechococcus/rRNA/*.aln; </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for i in ~/work/ProchlorococcusSynechococcus/rRNA/*.aln; </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>done > t_coffee_TCS.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>done > t_coffee_TCS.sh</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">--></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 t_coffee_TCS.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 t_coffee_TCS.sh</div></td></tr>
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Quentin
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Quentin: /* Annotation des ARNr */
2021-10-20T13:22:31Z
<p><span class="autocomment">Annotation des ARNr</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 13:22, 20 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for s in Prochlorococcus Synechococcus</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for s in Prochlorococcus Synechococcus</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat rnammer.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat rnammer.sh</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
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Quentin: /* Evaluation des Alignements */
2021-10-15T15:18:06Z
<p><span class="autocomment">Evaluation des Alignements</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:18, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Créez un fichier script pour lancer ''t_coffee'' avec ''sarray''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Créez un fichier script pour lancer ''t_coffee'' avec ''sarray''.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
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Quentin
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Quentin: /* Evaluation des Alignements */
2021-10-15T15:17:39Z
<p><span class="autocomment">Evaluation des Alignements</span></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:17, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.tcoffee.org/Projects/tcs/ TCS]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.tcoffee.org/Projects/tcs/ TCS]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"><del class="diffchange diffchange-inline">sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 t_coffee_TCS.sh</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>search_module T-COFFEE</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>search_module T-COFFEE</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td></tr>
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Quentin
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Quentin: /* Alignements des ARNr */
2021-10-15T15:17:17Z
<p><span class="autocomment">Alignements des ARNr</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 15:17, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pensez-vous que les alignements auraient été de meilleure qualité avec mafft-qinsi et l'option --maxiterate 1000?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pensez-vous que les alignements auraient été de meilleure qualité avec mafft-qinsi et l'option --maxiterate 1000?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==Evaluation des Alignements==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[http://www.tcoffee.org/Projects/tcs/ TCS] est un score d'évaluation d'alignement qui permet d'identifier dans un MSA les positions les plus correctes. Il a été démontré que ces positions sont les plus susceptibles d'être structurellement correctes et aussi les plus informatives lors de l'estimation des arbres phylogénétiques. La procédure d'évaluation et de filtrage TCS est implémentée dans le package '''T-Coffee''' et peut être utilisée pour évaluer et filtrer tout alignement de séquences multiples tiers.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[http://www.tcoffee.org/Projects/tcs/ TCS]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap">sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 t_coffee_TCS.sh</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">search_module T-COFFEE</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></pre></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">La commande est du type: </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> t_coffee -infile ~/work/ProchlorococcusSynechococcus/rRNA/ssu.aln -outfile essai -output score_ascii, aln, score_html</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Créez un fichier script pour lancer ''t_coffee'' avec ''sarray''.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">MSK</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><syntaxhighlight lang="bash"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">for i in ~/work/ProchlorococcusSynechococcus/rRNA/*.aln; </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">do </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> ip=$(basename $i .aln) </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> outfile="~/work/ProchlorococcusSynechococcus/rRNA/"$ip".ali"</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> echo "module load bioinfo/T-COFFEE_11.00.8cbe486; t_coffee -infile $i -output score_ascii, aln, score_html -outfile $outfile;" </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">done > t_coffee_TCS.sh</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></syntaxhighlight></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 t_coffee_TCS.sh</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">squeue -l -u $USER</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></pre></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><syntaxhighlight lang="bash"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">for i in ~/work/ProchlorococcusSynechococcus/rRNA/*.ali; </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">do </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> ip=$(basename $i .aln) </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> echo $ip</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> grep SCORE $i </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> grep -P "^cons +:" $i</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">done</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></syntaxhighlight></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Arbre avec seaview==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Arbre avec seaview==</div></td></tr>
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Quentin: /* Arbre SSU avec IQ-TREE */
2021-10-15T14:30:33Z
<p><span class="autocomment">Arbre SSU avec IQ-TREE</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:30, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pour seulement trouver le modèle le mieux adapté sans faire de reconstruction d'arbre, utilisez :</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pour seulement trouver le modèle le mieux adapté sans faire de reconstruction d'arbre, utilisez :</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">search_module iqtree</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>module load bioinfo/iqtree-1.6.7</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>module load bioinfo/iqtree-1.6.7</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>iqtree -s ~/work/ProchlorococcusSynechococcus/rRNA/ssu_renamed_simplified.phy -m MF -redo -AIC</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>iqtree -s ~/work/ProchlorococcusSynechococcus/rRNA/ssu_renamed_simplified.phy -m MF -redo -AIC</div></td></tr>
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Quentin: /* Alignements des ARNr */
2021-10-15T14:29:37Z
<p><span class="autocomment">Alignements des ARNr</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:29, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ssu</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ssu</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">search_module mafft</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>srun --pty bash</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>srun --pty bash</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>module load bioinfo/mafft-7.313</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>module load bioinfo/mafft-7.313</div></td></tr>
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Quentin: /* Annotation des ARNr */
2021-10-15T14:26:01Z
<p><span class="autocomment">Annotation des ARNr</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:26, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MSK</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><syntaxhighlight lang="bash"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for s in Prochlorococcus Synechococcus</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>for s in Prochlorococcus Synechococcus</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat rnammer.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat rnammer.sh</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></syntaxhighlight></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><pre style="color:blue;white-space: pre-wrap;white-space: -moz-pre-wrap;white-space: -pre-wrap;white-space: -o-pre-wrap"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 rnammer.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>sarray -J mkdb -o %j.out -e %j.err -t 01:00:00 --cpus-per-task=1 rnammer.sh</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>squeue -l -u <del class="diffchange diffchange-inline"><user></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>squeue -l -u <ins class="diffchange diffchange-inline">$USER</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
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Quentin: /* Introduction */
2021-10-15T14:20:43Z
<p><span class="autocomment">Introduction</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:20, 15 October 2021</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> ARNr 16S (1541 nucléotides chez E. coli2).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> ARNr 16S (1541 nucléotides chez E. coli2).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>--></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">Suivre : [http://silico.biotoul.fr/p/Atelier_Phylog%C3%A9nomique_Phylog%C3%A9nie_ARNr Phylogénie ARNr]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Annotation des ARNr==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Annotation des ARNr==</div></td></tr>
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Quentin: /* Liens */
2021-10-15T14:20:20Z
<p><span class="autocomment">Liens</span></p>
<a href="http://silico.biotoul.fr/site/index.php?title=Atelier_Phylog%C3%A9nomique_Phylog%C3%A9nie_ARNr&diff=8567&oldid=8566">Show changes</a>
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