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title: BioPerl HOWTOs
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<h2>Practical descriptions of BioPerl modules with a focus on common tasks.</h2>

<ul>
  <li><a href="/howtos/Beginners_HOWTO.html">Beginners HOWTO</a> - Introduction to BioPerl for biologists.</li>
  <li><a href="/howtos/Features_and_Annotations_HOWTO.html">Features and Annotations HOWTO</a> - Reading and writing detailed data associated with sequences.</li>
  <li><a href="/howtos/BlastPlus_HOWTO.html">BlastPlus HOWTO</a> - Create, manage, and query BLAST databases with NCBI blast+.</li>
  <li><a href="/howtos/EUtilities_Cookbook_HOWTO.html">EUtilities Cookbook HOWTO</a> - Simple script examples using Bio::DB::EUtilities.</li>
  <li><a href="/howtos/SearchIO_HOWTO.html">SearchIO HOWTO</a> - Parsing reports from sequence comparison programs like BLAST.</li>
  <li><a href="/howtos/SeqIO_HOWTO.html">SeqIO HOWTO</a> - Sequence file input and output, with script examples.</li>
  <li><a href="/howtos/Getting_Genomic_Sequences_HOWTO.html">Getting Genomic Sequences HOWTO</a> - Some examples of how to retrieve genomic sequences.</li>
  <li><a href="/howtos/AlignIO_and_SimpleAlign_HOWTO.html">AlignIO and SimpleAlign HOWTO</a> - Create and analyze alignments using BioPerl.</li>
  <li><a href="/howtos/Writing_BioPerl_Tests_HOWTO.html">Writing BioPerl Tests HOWTO</a> - A general guide on how to write BioPerl tests using Test::More.</li>
  <li><a href="/howtos/OBDA_Flat_databases_HOWTO.html">OBDA Flat Databases HOWTO</a> - Indexing local sequence files for fast retrieval using OBDA.</li>
  <li><a href="/howtos/Tiling_HOWTO.html">Tiling HOWTO</a> - Use SearchIO to create robust alignments.</li>
  <li><a href="/howtos/Local_Databases_HOWTO.html">Local Databases</a> - Indexing local sequence files for fast retrieval.</li>
  <li><a href="/howtos/OBDA_HOWTO.html">OBDA HOWTO</a> - Using OBDA, a universal and customizable sequence retrieval system.</li>
  <li><a href="/howtos/Restriction_Enzyme_Analysis_HOWTO.html">Restriction Enzyme Analysis HOWTO</a> - <i>in silico</i> restriction enzyme analysis.</li>
  <li><a href="/howtos/Short-read_assemblies_with_BWA_HOWTO.html">Short-read assemblies with BWA HOWTO</a> - Using the <i>bwa</i> assembler in BioPerl.</li>
  <li><a href="/howtos/Short-read_assemblies_with_maq_HOWTO.html">Short-read assemblies with maq HOWTO</a> - Using the <i>maq</i> assembler in BioPerl.</li>
  <li><a href="/howtos/Trees_HOWTO.html">Trees HOWTO</a> - Using BioPerl to analyze phylogenetic trees.</li>
  <li><a href="/howtos/EUtilities_Web_Service_HOWTO.html">EUtilities Web Service HOWTO</a> - Query NCBI Entrez via the EUtilities.</li>
  <li><a href="/howtos/PAML_HOWTO.html">PAML HOWTO</a> - Using the PAML package using BioPerl.</li>
  <li><a href="/howtos/PhyloXML_HOWTO.html">PhyloXML HOWTO</a> - Read and write phyloXML documents using BioPerl.</li>
  <li><a href="/howtos/Bioperl_Objects_HOWTO.html">Bioperl Objects HOWTO</a> - The common and uncommon objects that represent sequence.</li>
  <li><a href="/howtos/Simple_web_analysis_HOWTO.html">Simple Web Analysis HOWTO</a> - Submitting sequence data to Web forms and retrieving results.</li>
  <li><a href="/howtos/Best_Practices_HOWTO.html">Best Practices HOWTO</a> - The conventions to use when writing BioPerl code.</li>
  <li><a href="/howtos/Advanced_BioPerl_HOWTO.html">Advanced BioPerl HOWTO</a> - Notes on developing BioPerl code.</li>
  <li><a href="/howtos/PopGen_HOWTO.html">PopGen HOWTO</a> - Population genetics, molecular evolution, and BioPerl.</li>
  <li><a href="/howtos/SubmitPatch_HOWTO.html">SubmitPatch HOWTO</a> - The steps needed to get your modification to BioPerl into the code base.</li>
  <li><a href="/howtos/Nexml_HOWTO.html">Nexml HOWTO</a> - A guide on how to read and write Nexml documents using BioPerl.</li>
  <li><a href="/howtos/Glyphs_HOWTO.html">Glyphs HOWTO</a> - Extend Bio::Graphics using custom glyphs.</li>
  <li><a href="/howtos/BioGraphics_HOWTO.html">BioGraphics HOWTO</a> - Creating beautiful graphics for sequence display and annotation.</li>
  <li><a href="/howtos/Using_Git_HOWTO.html">Using Git HOWTO</a> - Using Git with BioPerl.</li>
  <li><a href="/howtos/Submitting_Issues_HOWTO.html">Submitting Issues HOWTO</a> - How we suggest submission of bugs and feature requests.</li>
  <li><a href="/howtos/Scrapbook_HOWTO.html">Scrapbook HOWTO</a> - Donated scraps of BioPerl code for you to reuse.</li>
  <!--
  This one is incomplete
  <li><a href="/howtos/PhylogeneticAnalysisPipeline_HOWTO.html">Phylogenetic Analysis Pipeline HOWTO
  A framework for phylogenetic analyses from gene set to gene family to alignment to phylogenetic inference.
  -->
</ul>

<h2>Instructions for BioPerl developers and maintainers</h2>

<ul>
  <li><a href="/howtos/split-new-distribution.html">Splitting a subset of modules into a new distribution</li>
</ul>

<h2>Common DNA and Protein Sequence Formats</h2>

<ul>
  <li><a href="https://bioperl.org/formats/sequence_formats/">Sequence format examples</li>
</ul>

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