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283b08d45f
* Move onebox gem in core library * Update template file path * Remove warning for onebox gem caching * Remove onebox version file * Remove onebox gem * Add sanitize gem * Require onebox library in lazy-yt plugin * Remove onebox web specific code This code was used in standalone onebox Sinatra application * Merge Discourse specific AllowlistedGenericOnebox engine in core * Fix onebox engine filenames to match class name casing * Move onebox specs from gem into core * DEV: Rename `response` helper to `onebox_response` Fixes a naming collision. * Require rails_helper * Don't use `before/after(:all)` * Whitespace * Remove fakeweb * Remove poor unit tests * DEV: Re-add fakeweb, plugins are using it * Move onebox helpers * Stub Instagram API * FIX: Follow additional redirect status codes (#476) Don’t throw errors if we encounter 303, 307 or 308 HTTP status codes in responses * Remove an empty file * DEV: Update the license file Using the copy from https://choosealicense.com/licenses/gpl-2.0/# Hopefully this will enable GitHub to show the license UI? * DEV: Update embedded copyrights * DEV: Add Onebox copyright notice * DEV: Add MIT license, convert COPYRIGHT.txt to md * DEV: Remove an incorrect copyright claim Co-authored-by: Jarek Radosz <jradosz@gmail.com> Co-authored-by: jbrw <jamie@goatforce5.org>
300 lines
71 KiB
XML
300 lines
71 KiB
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">Trace Archive</a></li><li><a href="/unigene" title=" Gene-centered clusters of transcripts and ESTs ">UniGene</a></li><li><a href="/unists" title=" Database of Sequence Tagged Sites ">UniSTS</a></li><li><a href="/guide/dna-rna/">All DNA & RNA Resources...</a></li></ul></li><li><a href="#data-software">Data & Software</a><ul class="actual-resources-submenu data-software"><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/Structure/CN3D/cn3d.shtml" title=" Program for viewing 3D structures and alignments ">Cn3D</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/WebSub/?tool=genbank" title=" Web tool for simple submissions of nucleotide sequences ">GenBank: BankIt</a></li><li><a href="/projects/Sequin/" title=" Software tool for complex submissions of nucleotide sequences ">GenBank: Sequin</a></li><li><a href="/genbank/tbl2asn2/" title=" Command-line program for submitting sequence data ">GenBank: tbl2asn</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/tools/gbench/" title=" Stand-alone application for analyzing sequence data ">Genome Workbench</a></li><li><a href="/tools/primer-blast/" title=" Designs PCR primers and analyzes them for target specificity using BLAST. ">Primer-BLAST</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="http://pubchem.ncbi.nlm.nih.gov/search/search.cgi" title=" Searches PubChem Compound by chemical structure ">PubChem Structure Search</a></li><li><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" title=" The SNP database tools page provides links to the general submission guidelines and to the submission handle request. ">SNP Submission Tool</a></li><li><a href="/sutils/splign/" title=" Tool for aligning transcripts to genomic DNA ">Splign</a></li><li><a href="/Structure/VAST/vast.html" title=" Tool that generates 3D structural alignments ">Vector Alignment Search Tool (VAST)</a></li><li><a href="/guide/data-software/">All Data & Software Resources...</a></li></ul></li><li><a href="#domains-structures">Domains & Structures</a><ul class="actual-resources-submenu domains-structures"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. ">BioSystems</a></li><li><a href="/Structure/CN3D/cn3d.shtml" title=" Program for viewing 3D structures and alignments ">Cn3D</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/structure/" title=" Database of 3D macromolecular structures derived from PDB ">Structure (Molecular Modeling Database)</a></li><li><a href="/Structure/VAST/vast.html" title=" Tool that generates 3D structural alignments ">Vector Alignment Search Tool (VAST)</a></li><li><a href="/guide/domains-structures/">All Domains & Structures Resources...</a></li></ul></li><li><a href="#genes-expression">Genes & Expression</a><ul class="actual-resources-submenu genes-expression"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. 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">Trace Archive</a></li><li><a href="/unists" title=" Database of Sequence Tagged Sites ">UniSTS</a></li><li><a href="/guide/genomes-maps/">All Genomes & Maps Resources...</a></li></ul></li><li><a href="#homology">Homology</a><ul class="actual-resources-submenu homology"><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/homologene" title=" Sets of homologous eukaryotic genes ">HomoloGene</a></li><li><a href="/proteinclusters" title=" Clusters of related proteins from prokaryotes and organelles ">Protein Clusters</a></li><li><a href="/guide/homology/">All Homology Resources...</a></li></ul></li><li><a href="#literature">Literature</a><ul class="actual-resources-submenu literature"><li><a href="/books" title=" Online biomedical books ">Bookshelf</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/nlmcatalog/journals" title=" Information on journals cited by NCBI records ">Journals in NCBI Databases</a></li><li><a href="/mesh" title=" Controlled vocabulary for MEDLINE ">MeSH Database</a></li><li><a href="/books/NBK143764/" title=" Introductory articles about NCBI resources ">NCBI Handbook</a></li><li><a href="/books/NBK3831/" title=" Online, searchable help documentation ">NCBI Help Manual</a></li><li><a href="/books/NBK1969/" title=" NCBI's monthly newsletter ">NCBI News</a></li><li><a href="/pubmed" title=" Biomedical literature abstracts ">PubMed</a></li><li><a href="/pmc/" title=" Free, full-text articles ">PubMed Central (PMC)</a></li><li><a href="/pubmed/clinical " title=" Directory of PubMed queries about clinical topics ">PubMed Clinical Queries</a></li><li><a href="/pubmedhealth/" title=" Reviews of clinical effectiveness research ">PubMed Health</a></li><li><a href="/guide/literature/">All Literature Resources...</a></li></ul></li><li><a href="#proteins">Proteins</a><ul class="actual-resources-submenu proteins"><li><a href="/biosystems/" title=" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. ">BioSystems</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/cdd" title=" Database of conserved protein domains represented by multiple sequence alignments ">Conserved Domain Database (CDD)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/books/NBK25501/ " title=" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system ">E-Utilities</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="/proteinclusters" title=" Clusters of related proteins from prokaryotes and organelles ">Protein Clusters</a></li><li><a href="/protein" title=" Protein sequence data ">Protein Database</a></li><li><a href="/refseq/" title=" Curated nucleotide and protein sequences produced by NCBI ">Reference Sequence (RefSeq)</a></li><li><a href="/guide/proteins/">All Proteins Resources...</a></li></ul></li><li><a href="#sequence-analysis">Sequence Analysis</a><ul class="actual-resources-submenu sequence-analysis"><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" title=" Tool for finding local regions of sequence similarity ">BLAST (Basic Local Alignment Search Tool)</a></li><li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download" title=" BLAST programs for a local computer ">BLAST (Stand-alone)</a></li><li><a href="/sutils/blink.cgi?mode=query" title=" Pre-computed reports showing proteins with similar sequences ">BLAST Link (BLink)</a></li><li><a href="/Structure/cdd/wrpsb.cgi" title=" Locates conserved domains within a protein sequence ">Conserved Domain Search Service (CD Search)</a></li><li><a href="/sutils/protmap.cgi" title=" Maps proteins from a COG/VOG back to its genome ">Genome ProtMap</a></li><li><a href="/tools/gbench/" title=" Stand-alone application for analyzing sequence data ">Genome Workbench</a></li><li><a href="/genomes/FLU/" title=" Data from the NIAID Influenza Genome Sequencing Project ">Influenza Virus</a></li><li><a href="/tools/primer-blast/" title=" Designs PCR primers and analyzes them for target specificity using BLAST. ">Primer-BLAST</a></li><li><a href="/sutils/static/prosplign/prosplign.html" title=" Tool for aligning proteins to genomic DNA ">ProSplign</a></li><li><a href="/sutils/splign/" title=" Tool for aligning transcripts to genomic DNA ">Splign</a></li><li><a href="/guide/sequence-analysis/">All Sequence Analysis Resources...</a></li></ul></li><li><a href="#taxonomy">Taxonomy</a><ul class="actual-resources-submenu taxonomy"><li><a href="/taxonomy" title=" The NCBI taxonomy tree in Entrez ">Taxonomy</a></li><li><a href="/Taxonomy/Browser/wwwtax.cgi?mode=Root" title=" Displays and links Entrez data to each taxonomic node ">Taxonomy Browser</a></li><li><a href="/Taxonomy/CommonTree/wwwcmt.cgi" title=" Creates custom taxonomic trees ">Taxonomy Common Tree</a></li><li><a href="/guide/taxonomy/">All Taxonomy Resources...</a></li></ul></li><li><a href="#training-tutorials">Training & Tutorials</a><ul class="actual-resources-submenu training-tutorials"><li><a href="/education/" title=" Central page providing links to tutorials and training materials ">NCBI Education Page</a></li><li><a href="/books/NBK143764/" title=" Introductory articles about NCBI resources ">NCBI Handbook</a></li><li><a href="/books/NBK3831/" title=" Online, searchable help documentation ">NCBI Help Manual</a></li><li><a href="/books/NBK1969/" title=" NCBI's monthly newsletter ">NCBI News</a></li><li><a href="/guide/training-tutorials/">All Training & Tutorials Resources...</a></li></ul></li><li><a href="#variation">Variation</a><ul class="actual-resources-submenu variation"><li><a href="/dbvar" title=" A database of genomic structural variation ">Database of Genomic Structural Variation (dbVar)</a></li><li><a href="/gap" title=" Genotype/Phenotype association studies ">Database of Genotypes and Phenotypes (dbGaP)</a></li><li><a href="/snp" title=" Database of nucleotide sequence polymorphisms ">Database of Single Nucleotide Polymorphisms (dbSNP)</a></li><li><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" title=" The SNP database tools page provides links to the general submission guidelines and to the submission handle request. 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<div class="rprt_all"><div class="rprt abstract"><div class="cit"><a href="#" title="Journal of molecular evolution." abstractLink="yes" alsec="jour" alterm="J Mol Evol.">J Mol Evol.</a> 1981;17(6):368-76.</div><h1>Evolutionary trees from DNA sequences: a maximum likelihood approach.</h1><div class="auths"><a href="/pubmed?term=Felsenstein%20J%5BAuthor%5D&cauthor=true&cauthor_uid=7288891">Felsenstein J</a>.</div><div class="abstr"><h3>Abstract</h3><div class=""><p>The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.</p></div></div><div class="aux"><div class="resc"><dl class="rprtid"><dt>PMID:</dt> <dd>7288891</dd> <dd> [PubMed - indexed for MEDLINE] </dd><dd> </dd></dl></div><div class="links"></div></div><div class="morecit"><h3><a title="Supplemental information" class="jig-ncbitoggler ui-ncbitoggler" href="#"><span class="ui-ncbitoggler-master-text">Publication Types, MeSH Terms, Substances</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></h3><div class="ui-ncbi-toggler-slave"><h4>Publication Types</h4><ul><li><a href="#" abstractLink="yes" alsec="ptyp" alterm="Research Support, U.S. Gov't, Non-P.H.S.">Research Support, U.S. Gov't, Non-P.H.S.</a></li></ul><h4>MeSH Terms</h4><ul><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Base Sequence*">Base Sequence*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Biological Evolution*">Biological Evolution*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Computers">Computers</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="DNA/genetics*">DNA/genetics*</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Mathematics">Mathematics</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Models, Biological">Models, Biological</a></li><li><a href="#" abstractLink="yes" alsec="mesh" alterm="Phylogeny">Phylogeny</a></li></ul><h4>Substances</h4><ul><li><a href="#" abstractLink="yes" alsec="subs" alterm="DNA">DNA</a></li></ul></div></div><div class="morecit"><h3><a title="Links to resources such as full text articles and biological data" class="jig-ncbitoggler ui-ncbitoggler" href="#"><span class="ui-ncbitoggler-master-text">LinkOut - more resources</span><span class="ui-icon ui-icon-triangle-1-e"></span></a></h3><div class="ui-ncbi-toggler-slave"><div class="linkoutlist"><h4>Other Literature Sources</h4><ul><li><a title="Free resource" href="http://www.scholaruniverse.com/ncbi-linkout?id=7288891" ref="itool=Abstract&PrId=3087&uid=7288891&db=pubmed&log$=linkoutlink&nlmid=0360051" target="_blank">COS Scholar Universe</a></li></ul></div></div></div><div id="comments_panel" data-recid="7288891" data-exp="true" data-rsys="1"><div id="comments_panel_head"><a id="coments_panel_anchor" href="/pubmedcommons/" name="comments">PubMed Commons home</a><h2><span id="show_comments" title="Shows comments">
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