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Atelier Phylogénomique - Revision history
2024-03-29T06:04:59Z
Revision history for this page on the wiki
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http://silico.biotoul.fr/site/index.php?title=Atelier_Phylog%C3%A9nomique&diff=10128&oldid=prev
Quentin: /* eggNOG */
2023-11-11T15:19:02Z
<p><span class="autocomment">eggNOG</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 15:19, 11 November 2023</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Seed orthologs (prefix.emapper.seed_orthologs) A file with the results from parsing the hits. Each row links a query with a seed ortholog. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Seed orthologs (prefix.emapper.seed_orthologs) A file with the results from parsing the hits. Each row links a query with a seed ortholog. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Annotations (prefix.emapper.annotations) A file with the results from the annotation phase. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Annotations (prefix.emapper.annotations) A file with the results from the annotation phase. </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><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: #ffa; color:black; font-size: smaller;"><div>rm eggnog-mapper.sh</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">if [[ -e eggnog-mapper.sh]]; then</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>for file in ~/work/<del class="diffchange diffchange-inline">Prochlorococcus</del>/<del class="diffchange diffchange-inline">peptide</del>/*.faa; </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>rm eggnog-mapper.sh</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">fi</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>for file in ~/work/<ins class="diffchange diffchange-inline">Zhang</ins>/<ins class="diffchange diffchange-inline">PEP</ins>/<ins class="diffchange diffchange-inline">Pr</ins>*.faa; </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>do</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>do</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> prefix=$(basename $file .faa)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> prefix=$(basename $file .faa)</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> echo "skip $output" </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> echo "skip $output" </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> else</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> else</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> echo "module load <del class="diffchange diffchange-inline">system</del>/Python-2.7.<del class="diffchange diffchange-inline">2</del>; module load bioinfo/<del class="diffchange diffchange-inline">eggnog</del>-mapper<del class="diffchange diffchange-inline">-</del>2.0.1; emapper.py -i $file --cpu 4 --output $prefix -m diamond" 1>> eggnog-mapper.sh</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> echo "module load <ins class="diffchange diffchange-inline">devel/python</ins>/Python-2.7.<ins class="diffchange diffchange-inline">18</ins>; module load bioinfo/<ins class="diffchange diffchange-inline">eggNOG</ins>-mapper<ins class="diffchange diffchange-inline">/</ins>2.0.1; emapper.py -i $file --cpu 4 --output $prefix -m diamond" 1>> eggnog-mapper.sh</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> fi</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> fi</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>done</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>done</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>squeue -l -u $USER</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>squeue -l -u $USER</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></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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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>les résultats sont dans : /home/formation/work/Prochlorococcus/eggNOG</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>les résultats sont dans : /home/formation/work/Prochlorococcus/eggNOG</div></td></tr>
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Quentin: /* eggNOG */
2023-11-11T15:09:43Z
<p><span class="autocomment">eggNOG</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 15:09, 11 November 2023</td>
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<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> emapper.py -i ~/work/Prochlorococcus/peptide/Aaaa.faa --cpu 4 --output Aaaa_NOG -m diamond</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> emapper.py -i ~/work/Prochlorococcus/peptide/Aaaa.faa --cpu 4 --output Aaaa_NOG -m diamond</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;">cp /usr/local/bioinfo/src/eggNOG-mapper/example_on_cluster/test_eggnog-mapper-2.0.1.sh eggnog-mapper-2.0.1.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;"></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;">module load devel/python/Python-2.7.18; module load bioinfo/eggNOG-mapper/2.0.1; emapper.py -i p53.fa --cpu 4 --output p53_maNOG -m diamond</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;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> -i FILE input FASTA file containing query sequences (proteins by default)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> -i FILE input FASTA file containing query sequences (proteins by default)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> --data_dir DIR Specify a path to the eggNOG-mapper databases. By default, data/ folder or the one specified by the EGGNOG_DATA_DIR environment variable. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> --data_dir DIR Specify a path to the eggNOG-mapper databases. By default, data/ folder or the one specified by the EGGNOG_DATA_DIR environment variable. </div></td></tr>
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Quentin: /* Matériel pédagogique */
2023-01-02T17:00:53Z
<p><span class="autocomment">Matériel pédagogique</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 17:00, 2 January 2023</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[http://phytools.org/eqg/Exercise_5.2/ Ancestral State Reconstruction with phytools]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[http://phytools.org/eqg/Exercise_5.2/ Ancestral State Reconstruction with phytools]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[http://www.phytools.org/eqg2015/asr.html Ancestral State Reconstruction with phytools2]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[http://www.phytools.org/eqg2015/asr.html Ancestral State Reconstruction with phytools2]</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;">*[http://genoweb.toulouse.inra.fr/~formation/M2_Phylogenomique/2022_supports/Reconstruction_etats_ancestraux.html Reconstruction_etats_ancestraux.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;">*[http://genoweb.toulouse.inra.fr/~formation/M2_Phylogenomique/2022_supports/Reconstruction_etats_ancestraux.Rmd Reconstruction_etats_ancestraux.Rmd]</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>anemone arome aster bleuet camelia capucine chardon clematite cobee coquelicot cosmos cyclamen dahlia digitale geranium gerbera glaieul hortensia iris jacinthe</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>anemone arome aster bleuet camelia capucine chardon clematite cobee coquelicot cosmos cyclamen dahlia digitale geranium gerbera glaieul hortensia iris jacinthe</div></td></tr>
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Quentin: /* Super-arbres */
2022-12-08T14:13:46Z
<p><span class="autocomment">Super-arbres</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 14:13, 8 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Commentez ce réseau par rapport aux autres arbres obtenus. Qu’en pensez-vous ?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Commentez ce réseau par rapport aux autres arbres obtenus. Qu’en pensez-vous ?</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;"></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;">'''ASTRAL'''</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;">* [https://github.com/smirarab/ASTRAL ASTRAL]</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://bioinfo.genotoul.fr/index.php/how-to-use/?software=How_to_use_SLURM_ASTRAL How_to_use_SLURM_ASTRAL]</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;">Nous pouvons utiliser entré du logiciel le fichier des arbres gènes/protéines concaténés.</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;">Un exemple de script de soumission: </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;">/home/formation/work/ProchlorococcusSynechococcus/phyloG/proteine/Astral/astral.sh</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>===Comparaison des arbres===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Comparaison des arbres===</div></td></tr>
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Quentin: /* Super-arbres */
2022-12-08T11:04:59Z
<p><span class="autocomment">Super-arbres</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 11:04, 8 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> sbatch --mem=20G ssuTree.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> sbatch --mem=20G ssuTree.sh</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>Voici l’arbre obtenu : </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Voici l’arbre obtenu :</div></td></tr>
<tr><td colspan="2"> </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>'''/home/formation/work/ProchlorococcusSynechococcus/phyloG/ssu_renamed_simplified.aln.treefile'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''/home/formation/work/ProchlorococcusSynechococcus/phyloG/ssu_renamed_simplified.aln.treefile'''</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 colspan="2" class="diff-lineno">Line 2,528:</td>
<td colspan="2" class="diff-lineno">Line 2,529:</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>Lançons les arbres protéiques. Pour cela faire un seul script que vous appellerez ind_pep_trees.sh et qui écrira toutes les commandes en bouclant sur chaque fichier d’entrée. Le but étant d’obtenir une ligne par commande iqtree sur un fichier d’alignement protéique. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Lançons les arbres protéiques. Pour cela faire un seul script que vous appellerez ind_pep_trees.sh et qui écrira toutes les commandes en bouclant sur chaque fichier d’entrée. Le but étant d’obtenir une ligne par commande iqtree sur un fichier d’alignement protéique. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Les fichiers d’input sont /home/formation/work/ProchlorococcusSynechococcus/phyloG/proteine/*_renamed.fas<del class="diffchange diffchange-inline">.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Les fichiers d’input sont <ins class="diffchange diffchange-inline">: </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''</ins>/home/formation/work/ProchlorococcusSynechococcus/phyloG/proteine/*_renamed.fas<ins class="diffchange diffchange-inline">'''</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>Il vous faut les copier dans votre work car sinon iqtree écrira les fichiers d'output sur le répertoire du compte de formation et pas dans le votre...</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Il vous faut les copier dans votre work car sinon iqtree écrira les fichiers d'output sur le répertoire du compte de formation et pas dans le votre...</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 2,537:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pour vous aider inspirez vous de la réponse à la question "How to generate an sarray command file with bash for single (fastq) file ?" sur la page http://bioinfo.genotoul.fr/index.php/faq/bioinfo_tips_faq/.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Pour vous aider inspirez vous de la réponse à la question "How to generate an sarray command file with bash for single (fastq) file ?" sur la page http://bioinfo.genotoul.fr/index.php/faq/bioinfo_tips_faq/.</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>'''Attention à bien spécifier -nt 1. Si vous souhaitez utiliser plus d’un CPU il faut le réserver avec l’option --cpus-per-task dans la commande sbatch / sarray. Pas besoin d’augmenter la RAM pour les protéines. Pensez aussi à mettre -AIC comme critère de sélection de modèle.'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Attention à bien spécifier -nt 1. Si vous souhaitez utiliser plus d’un CPU il faut le réserver avec l’option --cpus-per-task dans la commande sbatch / sarray. Pas besoin d’augmenter la RAM pour les protéines. Pensez aussi à mettre <ins class="diffchange diffchange-inline">'''</ins>-AIC<ins class="diffchange diffchange-inline">''' </ins>comme critère de sélection de modèle.'''</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>Regarder le contenu de ind_pep_trees.sh. Est-il correct ?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Regarder le contenu de ind_pep_trees.sh. Est-il correct ?</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;">Remarque, il n'est pas toujours utile de tester l'ensemble des modèles, vous pouvez faire une pré-sélection avec l'option -mset et/ou -madd. Exemple '''-mset WAG,JTT,LG'''.</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>Rajouter la première ligne obligatoire sur genologin avec vi par exemple : </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Rajouter la première ligne obligatoire sur genologin avec vi par exemple : </div></td></tr>
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Quentin: /* Super-arbres */
2022-12-08T10:30:22Z
<p><span class="autocomment">Super-arbres</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 10:30, 8 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> sbatch --mem=20G ssuTree.sh</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> sbatch --mem=20G ssuTree.sh</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>Voici l’arbre obtenu : /home/formation/work/ProchlorococcusSynechococcus/phyloG/ssu_renamed_simplified.aln.treefile</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Voici l’arbre obtenu : </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''</ins>/home/formation/work/ProchlorococcusSynechococcus/phyloG/ssu_renamed_simplified.aln.treefile<ins class="diffchange diffchange-inline">'''</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>'''A vous :''' </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''A vous :''' </div></td></tr>
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Quentin: /* Phylogénie basée sur les séquences des ARNr */
2022-12-08T10:09:37Z
<p><span class="autocomment">Phylogénie basée sur les séquences des ARNr</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 10:09, 8 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> La petite sous-unité ribosomique 30S contient l'ARNr suivant :</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> La petite sous-unité ribosomique 30S contient l'ARNr suivant :</div></td></tr>
<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: #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;"><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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Suivre </ins>: [<ins class="diffchange diffchange-inline">http://silico.biotoul.fr/p/Atelier_Phylog%C3%A9nomique_Phylog%C3%A9nie_ARNr </ins>Phylogénie ARNr]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Ne pas suivre </del>: [<del class="diffchange diffchange-inline">Phylogénie ARNr </del>Phylogénie ARNr]</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: #ffa; color:black; font-size: smaller;"><div> </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><!--</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: #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: /* Arbre espèces: préparation des fichiers */
2022-12-07T21:56:55Z
<p><span class="autocomment">Arbre espèces: préparation des fichiers</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:56, 7 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Arbre espèces: préparation des fichiers==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Arbre espèces: préparation des fichiers==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Support de cours :''' [http://genoweb.toulouse.inra.fr/~formation/M2_Phylogenomique/2020_supports/ supports]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Support de cours <ins class="diffchange diffchange-inline">1 </ins>:''' [http://genoweb.toulouse.inra.fr/~formation/M2_Phylogenomique/2020_supports<ins class="diffchange diffchange-inline">/ supports]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''Support de cours 2 :''' [http://genoweb.toulouse.inra.fr/~formation/M2_Phylogenomique/2022_supports</ins>/ supports]</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>Nous allons utiliser un sous ensemble de gènes concervés chez ''Prochlorococcus'' et ''Synechococcus'' pour expérimenter les différentes méthodes de reconstruction phylogénomiques. Nous nous initierons à la comparaison d’arbres.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Nous allons utiliser un sous ensemble de gènes concervés chez ''Prochlorococcus'' et ''Synechococcus'' pour expérimenter les différentes méthodes de reconstruction phylogénomiques. Nous nous initierons à la comparaison d’arbres.</div></td></tr>
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Quentin: s
2022-12-07T09:35:57Z
<p>s</p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 09:35, 7 December 2022</td>
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<td colspan="2" class="diff-lineno">Line 2,053:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> La petite sous-unité ribosomique 30S contient l'ARNr suivant :</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> La petite sous-unité ribosomique 30S contient l'ARNr suivant :</div></td></tr>
<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 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;">Suivre : [http://silico.biotoul.fr/p/Atelier_Phylog%C3%A9nomique_Phylog%C3%A9nie_ARNr Phylogénie ARNr]</ins></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: #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><del class="diffchange diffchange-inline">Suivre </del>: [<del class="diffchange diffchange-inline">http://silico.biotoul.fr/p/Atelier_Phylog%C3%A9nomique_Phylog%C3%A9nie_ARNr </del>Phylogénie ARNr]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Ne pas suivre </ins>: [<ins class="diffchange diffchange-inline">Phylogénie ARNr </ins>Phylogénie ARNr]</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><!--</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: /* IQ-TREE */
2022-12-06T17:57:42Z
<p><span class="autocomment">IQ-TREE</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 17:57, 6 December 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Documentation : http://www.iqtree.org/doc/</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Documentation : http://www.iqtree.org/doc/</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;">Documentation : [http://www.iqtree.org/doc/Substitution-Models "Substitution-Models"]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='bash'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='bash'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>mkdir ~/work/ProchlorococcusSynechococcus/phyloG/</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>mkdir ~/work/ProchlorococcusSynechococcus/phyloG/</div></td></tr>
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