1531 lines
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HTML
1531 lines
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<a href="/obidoc/docs/about/" class="">About</a>
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<a role="button" class="active">File formats</a>
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<label for="section-933c2e64b905b84e22aa5273cea2d0bd" class="flex justify-between">
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<a role="button" class="">Sequence file formats</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/formats/fasta/" class="">FASTA file format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/formats/fastq/" class="">FASTQ file format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/formats/genbank/" class="">GenBank Flat File format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/formats/embl/" class="">EMBL Flat File format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/file_format/sequence_files/csv/" class="">CSV format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/formats/json/" class="">JSON format</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
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<ul>
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<label for="section-0258ae1c222f9a38cc1b75254c93b0f4" class="flex justify-between">
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<a role="button" class="">Taxonomy file formats</a>
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<li>
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<a href="/obidoc/docs/file_format/taxonomy_file/csv_taxdump/" class="">CSV formatted taxdump</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/" class="">NCBI taxdump</a>
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<ul>
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</ul>
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</ul>
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<li>
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<a href="/obidoc/formats/csv/" class="">The CSV format</a>
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<ul>
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</ul>
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</li>
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</ul>
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<label for="section-70b1e6e5ec7f3ccab643155fa50659b6" class="flex justify-between">
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<a role="button" class="">Patterns</a>
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<li>
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<a href="/obidoc/docs/patterns/regular/" class="">Regular Expressions</a>
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<li>
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<a href="/obidoc/docs/patterns/dnagrep/" class="">DNA Patterns</a>
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</ul>
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<a role="button" class="">The OBITools4 commands</a>
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<a href="/obidoc/docs/commands/options/" class="">Shared command options</a>
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<ul>
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<a role="button" class="">Basics</a>
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<li>
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<a href="/obidoc/obitools/obiannotate/" class="">obiannotate</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obicomplement/" class="">obicomplement</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiconvert/" class="">obiconvert</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obicount/" class="">obicount</a>
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<ul>
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<li>
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<a href="/obidoc/obitools/obicsv/" class="">obicsv</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obidemerge/" class="">obidemerge</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
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<ul>
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<li>
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<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
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<ul>
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</ul>
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</ul>
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<input type="checkbox" id="section-dbdf1bb5377572439394e60e08c30f50" class="toggle" />
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<label for="section-dbdf1bb5377572439394e60e08c30f50" class="flex justify-between">
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<a role="button" class="">Demultiplexing samples</a>
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</label>
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<li>
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<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
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<ul>
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</ul>
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<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
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<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
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<a role="button" class="">Sequence alignments</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
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<ul>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-7433746525d8c2b29b033f765c869acd" class="toggle" />
|
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<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
|
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<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obitag/" class="">obitag</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-5746f699d10490780dec8e30ab2dd3ce" class="toggle" />
|
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<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
|
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<a role="button" class="">Taxonomy</a>
|
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-3f50c4fe7ab436a56ae92897d5444956" class="toggle" />
|
|
<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
|
|
<a role="button" class="">Advanced tools</a>
|
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</label>
|
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<ul>
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<li>
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<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
|
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<ul>
|
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-549be3934679fcb82a232f6bd5435563" class="toggle" />
|
|
<label for="section-549be3934679fcb82a232f6bd5435563" class="flex justify-between">
|
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<a role="button" class="">Others</a>
|
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</label>
|
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<ul>
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<li>
|
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<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
|
|
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|
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<ul>
|
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</ul>
|
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</li>
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</ul>
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</li>
|
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<li>
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<input type="checkbox" id="section-ceca4455173761e30cbc0a6dc2327167" class="toggle" />
|
|
<label for="section-ceca4455173761e30cbc0a6dc2327167" class="flex justify-between">
|
|
<a role="button" class="">Experimentals</a>
|
|
</label>
|
|
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<ul>
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<li>
|
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|
<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
|
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<ul>
|
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</ul>
|
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</li>
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<li>
|
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|
|
<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
|
|
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|
|
<ul>
|
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|
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</ul>
|
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</li>
|
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<li>
|
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|
|
<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
|
|
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|
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<ul>
|
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|
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</ul>
|
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</li>
|
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</ul>
|
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</li>
|
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<li>
|
|
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|
|
<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
|
|
|
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|
|
</li>
|
|
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|
|
</ul>
|
|
|
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</li>
|
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<li>
|
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|
|
<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
|
|
<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
|
|
<a role="button" class="">Cookbook</a>
|
|
</label>
|
|
|
|
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|
|
<ul>
|
|
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|
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<li>
|
|
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|
|
<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
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</li>
|
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|
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|
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<li>
|
|
|
|
|
|
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|
|
|
<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
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</li>
|
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|
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<li>
|
|
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|
|
<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
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</li>
|
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|
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|
|
<li>
|
|
|
|
|
|
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|
|
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|
|
<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
|
|
|
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|
|
<ul>
|
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|
|
</ul>
|
|
|
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</li>
|
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|
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<li>
|
|
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|
|
<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
|
|
|
|
|
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|
|
<ul>
|
|
|
|
</ul>
|
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|
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</li>
|
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</ul>
|
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</li>
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<li>
|
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|
<span>Programming OBITools</span>
|
|
|
|
|
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|
|
<ul>
|
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|
|
<li>
|
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|
|
<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
|
|
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|
|
<ul>
|
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</ul>
|
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</li>
|
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<li>
|
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|
|
<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" />
|
|
<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
|
|
<a href="/obidoc/docs/programming/lua/" class="">Lua: for scripting OBITools</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
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<li>
|
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|
|
<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
|
|
<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
|
|
<a role="button" class="">Obitools Classes</a>
|
|
</label>
|
|
|
|
|
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|
|
<ul>
|
|
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|
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<li>
|
|
|
|
|
|
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|
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|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
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|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
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|
|
<li>
|
|
|
|
|
|
|
|
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|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
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<li>
|
|
|
|
|
|
|
|
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|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
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|
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<li>
|
|
|
|
|
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|
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|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
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</li>
|
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</ul>
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</li>
|
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</ul>
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</li>
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</ul>
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</li>
|
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</ul>
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</li>
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</ul>
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</nav>
|
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<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
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</div>
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</aside>
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<div class="book-page">
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<header class="book-header">
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<div class="flex align-center justify-between">
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<label for="menu-control">
|
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<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
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<h3>File formats</h3>
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<label for="toc-control">
|
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|
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<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
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<aside class="hidden clearfix">
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<nav id="TableOfContents"></nav>
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<article class="markdown book-article"></article>
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<footer class="book-footer">
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<div class="flex flex-wrap justify-between">
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