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It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy-Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is th...","author":[{"@context":"https://schema.org","@type":"Person","name":"Ferran Palero"}],"contributor":[],"dateCreated":"2013-07-25","dateModified":"2022-05-23","datePublished":null,"headline":"MICROSATELIGHT--pipeline to expedite microsatellite analysis","inLanguage":"en","keywords":[],"locationCreated":null,"publication":"The Journal of heredity","publisher":{"@context":"https://schema.org","@type":"Organization","name":"ncbi.nlm.nih.gov"},"image":null,"thumbnailUrl":null,"url":"https://www.academia.edu/4104951/MICROSATELIGHT_pipeline_to_expedite_microsatellite_analysis","sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":null}]}</script><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/single_work_page/loswp-102fa537001ba4d8dcd921ad9bd56c474abc201906ea4843e7e7efe9dfbf561d.css" /><link rel="stylesheet" media="all" 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data-author-id="32805539" href="https://ucriverside.academia.edu/DavidReznick">David Reznick</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Molecular Ecology Resources, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"MEGASAT: automated inference of microsatellite genotypes from sequence data","attachmentId":74269291,"attachmentType":"pdf","work_url":"https://www.academia.edu/61115782/MEGASAT_automated_inference_of_microsatellite_genotypes_from_sequence_data","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/61115782/MEGASAT_automated_inference_of_microsatellite_genotypes_from_sequence_data"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="3280460" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/3280460/Normalization_and_binning_of_historical_and_multi_source_microsatellite_data_overcoming_the_problems_of_allele_size_shift_with_allelogram">Normalization and binning of historical and multi-source microsatellite data: overcoming the problems of allele size shift with allelogram</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="3779621" href="https://independent.academia.edu/CarlManaster">Carl Manaster</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Molecular Ecology Resources, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">Microsatellite allele data have long been plagued by size shifts that can at best make it difficult to accurately assign genotypes to allele products, and at worse can cause whole batches of data from different instruments, dates or laboratories to be incorrectly assigned. Although modern genotyping technology (capillary electrophoresis) has overcome many of these problems, concern remains regarding the consistency of scores within a laboratory over time and between laboratories when combining data from multiple sources into a single analysis. There remain a large number of laboratories using older technologies or combining data from multiple sources. In addition, thousands of data sets that could potentially be expanded as samples become available are generally regarded as unusable because of the effort that would be required to validate congruence of genotypes from old and new data sets. 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Authors","attachmentId":32801666,"attachmentType":"pdf","work_url":"https://www.academia.edu/5779661/A_program_for_the_population_analysis_of_allotetraploid_microsatellite_data_Authors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/5779661/A_program_for_the_population_analysis_of_allotetraploid_microsatellite_data_Authors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="76023685" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" 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18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/76023685/Determining_relative_microsatellite_allele_frequencies_in_pooled_DNA_samples"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="14062914" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/14062914/Accurate_determination_of_microsatellite_allele_frequencies_in_pooled_DNA_samples">Accurate determination of microsatellite allele frequencies in pooled DNA samples</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33080553" href="https://umcu.academia.edu/HugoSchnack">Hugo Schnack</a></div><p class="ds-related-work--metadata ds2-5-body-xs">European Journal of Human Genetics, 2004</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Accurate determination of microsatellite allele frequencies in pooled DNA samples","attachmentId":44645741,"attachmentType":"pdf","work_url":"https://www.academia.edu/14062914/Accurate_determination_of_microsatellite_allele_frequencies_in_pooled_DNA_samples","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/14062914/Accurate_determination_of_microsatellite_allele_frequencies_in_pooled_DNA_samples"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="23069555" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/23069555/GEVALT_an_integrated_software_tool_for_genotype_analysis">GEVALT: an integrated software tool for genotype analysis</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="37445686" href="https://telaviv.academia.edu/RonShamir">Ron Shamir</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC bioinformatics, 2007</p><p class="ds-related-work--abstract ds2-5-body-sm">Genotype information generated by individual and international efforts carries the promise of revolutionizing disease studies and the association of phenotypes with alleles and haplotypes. Given the enormous amounts of public genotype data, tools for analyzing, interpreting and visualizing these data sets are of critical importance to researchers. In past works we have developed algorithms for genotypes phasing and tag SNP selection, which were shown to be quick and accurate. Both algorithms were available until now only as batch executables. Here we present GEVALT (GEnotype Visualization and ALgorithmic Tool), a software package designed to simplify and expedite the process of genotype analysis, by providing a common interface to several tasks relating to such analysis. GEVALT combines the strong visual abilities of Haploview with our quick and powerful algorithms for genotypes phasing (GERBIL), tag SNP selection (STAMPA) and permutation testing for evaluating significance of assoc...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"GEVALT: an integrated software tool for genotype analysis","attachmentId":43572780,"attachmentType":"pdf","work_url":"https://www.academia.edu/23069555/GEVALT_an_integrated_software_tool_for_genotype_analysis","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/23069555/GEVALT_an_integrated_software_tool_for_genotype_analysis"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":31626192,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":31626192,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_31626192" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. 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data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Robust Statistical Method to Detect Null Alleles in Microsatellite and SNP Datasets in Both Panmictic and Inbred Populations","attachmentId":6846113,"attachmentType":"pdf","work_url":"https://www.academia.edu/1043051/A_Robust_Statistical_Method_to_Detect_Null_Alleles_in_Microsatellite_and_SNP_Datasets_in_Both_Panmictic_and_Inbred_Populations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/1043051/A_Robust_Statistical_Method_to_Detect_Null_Alleles_in_Microsatellite_and_SNP_Datasets_in_Both_Panmictic_and_Inbred_Populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" 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analysis","attachmentId":69873732,"attachmentType":"pdf","work_url":"https://www.academia.edu/52766829/Merging_microsatellite_data_enhanced_methodology_and_software_to_combine_genotype_data_for_linkage_and_association_analysis","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/52766829/Merging_microsatellite_data_enhanced_methodology_and_software_to_combine_genotype_data_for_linkage_and_association_analysis"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="6" data-entity-id="55183996" data-sort-order="default"><a 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analysis","attachmentId":71176237,"attachmentType":"pdf","work_url":"https://www.academia.edu/55183996/genotypeR_An_integrated_r_package_for_single_nucleotide_polymorphism_genotype_marker_design_and_data_analysis","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/55183996/genotypeR_An_integrated_r_package_for_single_nucleotide_polymorphism_genotype_marker_design_and_data_analysis"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="7" data-entity-id="62670408" data-sort-order="default"><a class="ds-related-work--title 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Data","attachmentId":75356438,"attachmentType":"pdf","work_url":"https://www.academia.edu/62670408/PolyMorphPredict_A_Universal_Web_Tool_for_Rapid_Polymorphic_Microsatellite_Marker_Discovery_From_Whole_Genome_and_Transcriptome_Data","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/62670408/PolyMorphPredict_A_Universal_Web_Tool_for_Rapid_Polymorphic_Microsatellite_Marker_Discovery_From_Whole_Genome_and_Transcriptome_Data"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="8" data-entity-id="7469649" 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