1090 lines
52 KiB
HTML
1090 lines
52 KiB
HTML
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<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4201177/css/4121862/3974050/3917732/251717/4092826/3428953/14534/45193/3534283/4128070/3894326/4005757/2867781/3621797.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4201177/css/3529741/3529739.css" media="print" /><script type="text/javascript">
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The NCBI web site requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
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<div class="usa-banner-content usa-grid usa-accordion-content" id="gov-banner-top" aria-hidden="true">
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<strong>The .gov means it's official.</strong>
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<br />
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Federal government websites often end in .gov or .mil. Before
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sharing sensitive information, make sure you're on a federal
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government site.
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<br />
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The <strong>https://</strong> ensures that you are connecting to the
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official website and that any information you provide is encrypted
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and transmitted securely.
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</div>
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</section>
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<div class="usa-overlay"></div>
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<header class="ncbi-header" role="banner" data-section="Header">
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<div class="usa-grid">
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<div class="usa-width-one-whole">
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<div class="ncbi-header__logo">
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<a href="/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
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</a>
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</div>
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<div class="ncbi-header__account">
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<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
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<span class="fa fa-user" aria-hidden="true">
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<span class="sr-only">Show account info</span>
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<div class="ncbi-popup-anchor">
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<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
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</svg>
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<span class="usa-sr-only">Close</span></button>
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<h4>Account</h4>
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</div>
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<div class="account-user-info">
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Logged in as:<br />
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<b><span class="username" id="uname_long">username</span></b>
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<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
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<li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li>
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</div>
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</div>
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</div>
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</div>
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</header>
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<div role="navigation" aria-label="access keys">
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<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
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<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
|
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<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
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<section data-section="Alerts">
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<div class="ncbi-alerts-placeholder"></div>
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</section>
|
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</div>
|
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</div>
|
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<!--/.header-->
|
||
<div class="header">
|
||
<div class="res_logo"><h1 class="res_name"><a href="/tools/msaviewer/" title="Multiple Sequence Alignment Viewer home">Multiple Sequence Alignment Viewer</a></h1><h2 class="res_tagline"></h2></div>
|
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|
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<label for="searchbarlite">Search NCBI </label>
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<input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFAppLayout" /><input type="hidden" name="p$st" id="p$st" value="tools" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/staticsites/sviewer/sviewerdoc@1.22" disabled="disabled" type="hidden" /></form>
|
||
|
||
|
||
</div>
|
||
<div class="nav_and_browser">
|
||
<div class="localnav"><ul class="jig-ncbilocalnav">
|
||
<li><a href="#">MSA Viewer</a><ul>
|
||
<li><a href="/projects/msaviewer/">Multiple Sequence Alignment Viewer application</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#">General</a><ul>
|
||
<li><a href="/tools/msaviewer/about/">About</a></li>
|
||
<li><a href="/tools/msaviewer/embedding-api/">MSA Viewer Embedding API</a></li>
|
||
<li><a href="/tools/msaviewer/release-notes/">Release Notes</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#">Help</a><ul>
|
||
<li><a href="/tools/msaviewer/tutorial1">Guide to Using the MSA Viewer</a></li>
|
||
<li><a href="/tools/msaviewer/video/">Video Tutorials</a></li>
|
||
<li><a href="/tools/msaviewer/legend/">Legend</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#">Demo Pages</a><ul>
|
||
<li><a href="/projects/msaviewer/demo/demo_static.html">Static embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_dynamic.html">Dynamic embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_sort.html">Sorting parameters embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_consensus.html">Consensus parameters embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_events.html">Event Handling</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_coloring.html">Coloring</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_columns.html">Customizing Columns</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_mapping.html">Alignment Coordinate Transformation</a> </li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#">Related Resources</a><ul>
|
||
<li><a href="/projects/sviewer/">Sequence Viewer</a></li>
|
||
<li><a href="/projects/treeview/">Tree Viewer</a></li>
|
||
</ul>
|
||
</li>
|
||
</ul></div>
|
||
</div>
|
||
|
||
<!-- was itemctrl -->
|
||
<div class="container">
|
||
<div id="maincontent" class="content col twelve_col last">
|
||
<div class="col1">
|
||
<h1 id="release-notes-for-msa-viewer-ver">Release Notes for MSA Viewer Version 1.25.0 (October 31, 2023)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>The full page MSA viewer displays an updated header and footer</li>
|
||
<li>Improved performance due to use of updated technical components (PubSeq Gateway, Stable Components version 28)</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_1">Release Notes for MSA Viewer Version 1.24.0 (June 13, 2023)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_1">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Improved default rendering of MSA Viewer on mobile or small screens</li>
|
||
<li>Minor tweaks to behavior of alignment info popups</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_2">Release Notes for MSA Viewer Version 1.23.0 (February 28, 2023)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_2">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>MSA is configured to display pairwise assembly-assembly alignments from the <a href="/genome/cgv/">Comparative Genome Viewer (CGV)</a></li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_3">Release Notes for MSA Viewer Version 1.22.0 (April 7, 2022)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_3">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New ability to <a href="/tools/msaviewer/tutorial1/#Search">search</a> for sequence strings in the anchor/consensus row using the Find button on the toolbar</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_4">Release Notes for MSA Viewer Version 1.21.0 (November 1, 2021)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_4">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Gene and protein annotation on the panorama panel can now be hidden using the collape/expand caret button or by adding &collapse_pan to the URL</li>
|
||
<li>Improvements to display of the toolbar on mobile screens</li>
|
||
<li>Supports <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2021/09/02/64-bit-gis/">64-bit NCBI GI accessions</a></li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed sorting of "Identity" and "Coverage" columns in the Rows dialog</li>
|
||
<li>Additional minor bug fixes</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_5">Release Notes for MSA Viewer Version 1.20.0 (March 29, 2021)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_5">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New option to adjust column width from the Columns configure dialog </li>
|
||
<li>New ability to access the context menu (e.g. set anchor, hide rows) by right-clicking your cursor over any column</li>
|
||
<li>New ability to select to highlight a row by clicking within any column; multiple rows can be selected using the Ctrl or Shift keys</li>
|
||
<li>Warning message added alerting users that MSA currently does not support views of alignments containing both nucleotide and protein sequences</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_1">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Additional minor bug fixes</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_6">Release Notes for MSA Viewer Version 1.19.0 (January 14, 2021)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_6">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New option to show <a href="/tools/msaviewer/tutorial1/#Columns">columns</a> reporting percent identity, percent coverage, and number of mismatches relative to the consensus or anchor sequence (must show consensus or set an anchor row to see data)</li>
|
||
<li>New option to show column reporting Gene symbol (for RefSeq accessions)</li>
|
||
<li>New option to click within the ruler to temporarily set a vertical guideline at a single sequence position</li>
|
||
<li>Updated data model with improved handling of sequence alignments with large amounts of insertions</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_2">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Additional minor bug fixes</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_7">Release Notes for MSA Viewer Version 1.18.0 (October 27, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_7">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New ability to remove or add <a href="/tools/msaviewer/tutorial1/#Columns">columns</a> using the Column dialog found on the top toolbar</li>
|
||
<li>Option to add columns for country, host, source (isolation source), or date (collection date)</li>
|
||
<li>Column type and order can be specified in the embedding API</li>
|
||
<li>Complete text is shown in an information box when you hover over text that is longer than the width of a column</li>
|
||
<li>Sort rows by column by clicking on the column header</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_8">Release Notes for MSA Viewer Version 1.17.0 (September 17, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_8">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Additional sorting options in the Rows edit dialog (country, host, isolation source, collection date)</li>
|
||
<li>New ability to click and drag to selecta region on the ruler above the alignment and zoom directly to that range</li>
|
||
<li>New ability to download consensus row sequence from the right-click context menu</li>
|
||
<li>Rows in the alignment can now be selected in bulk using the Shift key</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_3">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Anchor row will no longer be shown in the Rows edit dialog as it cannot be hidden</li>
|
||
<li>Fixed bugs in the behavior of the tooltips</li>
|
||
<li>Additional bug fixes and tech debt</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_9">Release Notes for MSA Viewer Version 1.16.0 (August 10, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_9">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New ability to sort columns in the alignment alphanumerically</li>
|
||
<li>Improved language in reporting insertions and gaps in row position tooltips</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_4">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed errors in rendering the ruler for short sequence alignments</li>
|
||
<li>Fixed ability to download FASTA alignment files from larger BLAST alignments</li>
|
||
<li>Ambiguous bases will no longer be colored as mismatches in the alignment</li>
|
||
<li>Additional bug fixes and tech debt</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_10">Release Notes for MSA Viewer Version 1.15.0 (July 7, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_10">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New ability to <a href="/tools/msaviewer/tutorial1/#Hiding">hide rows</a> in the alignment from view via the right-click menu or an "edit rows" dialog that can be launched from the top toolbar</li>
|
||
<li>Hidden rows are not shown in the image or FASTA alignment downloads and are hidden in shared links</li>
|
||
<li>Shown rows are reported on the status bar on the bottom right of the alignment</li>
|
||
<li>FASTA download is updated to show the full defline including organism name and title from the GenBank record where available</li>
|
||
<li>Consensus sequence can be downloaded as part of the FASTA alignment file when the consensus is shown in the view</li>
|
||
<li>"Master" row is renamed to <a href="/tools/msaviewer/tutorial1/#Master">"Anchor"</a></li>
|
||
<li>Updated icon for Tools menu</li>
|
||
<li>Performance improvements in tooltips from incorporating WebAssembly </li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_5">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Minor bug fixes</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_11">Release Notes for MSA Viewer Version 1.14.0 (May 26, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_11">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New ability to download the alignment view in PDF or SVG format</li>
|
||
<li>Updated public documentation (e.g. <a href="/tools/msaviewer/tutorial1/">Guide to Using the MSA Viewer</a>) </li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_6">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>"Show identical bases as dots" checkbox is now shown only when master or consensus is set</li>
|
||
<li>Ambiguous bases will no longer be counted as mismatches in the alignment or panorama view</li>
|
||
<li>Additional minor bug fixes </li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_12">Release Notes for MSA Viewer Version 1.13.1 (May 4, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_12">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Added an option in the Tools menu and right-click context menu to show/hide a consensus row </li>
|
||
<li>The query sequence will be automatically set as master for alignments coming from NCBI BLAST</li>
|
||
<li>Coloring options for alignments can now be accessed from the top toolbar</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_7">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>"Show identical bases as dots" works when either a consensus or master is set</li>
|
||
<li>Fixed a bug in the back button</li>
|
||
<li>Fixed an image rendering issue when using "Column Quality Score"</li>
|
||
<li>Fixed a bug in coloring menu options for uploaded nucleotide files</li>
|
||
<li>Additional minor bug fixes </li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_13">Release Notes for MSA Viewer Version 1.12.0 (March 30, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_13">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Ambiguous nucleotides or residues ('N' or 'X') are now excluded in score calculations and colored dark grey when using the "Frequency Based Difference" and "Column Quality Score" coloring methods</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_8">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed isses that resulted in errors in the multiple alignment of <a href="/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Wuhan seafood market pneumonia virus, taxid:2697049&SLen_i=29000 TO 30000">SARS coronavirus 2 sequences</a> at the NCBI Virus data hub</li>
|
||
<li>Fixed ability to view SRA alignments from BLAST in the MSA viewer</li>
|
||
<li>Fixed link from SRA reads in alignments to the SRA database</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_14">Release Notes for MSA Viewer Version 1.11 (January 16, 2020)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_14">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Added support for stop character * in uploaded FASTA alignment files</li>
|
||
<li>Added support for pipe | symbol in id of uploaded FASTA alignment files</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_9">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed bugs in coordination of panorama and alignment views</li>
|
||
<li>Fixed glitches in rendering of the master row</li>
|
||
<li>Fixed bugs in rendering results in COBALT</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_15">Release Notes for MSA Viewer Version 1.10 (March 19, 2019)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_15">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>“Link to View” now uses usa.gov domain</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_10">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed issue with PDB ID in GI-less database</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_16">Release Notes for MSA Viewer Version 1.9 (October 25, 2018)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_16">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Flexible vertical space allocation implemented</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_11">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Projected features in proteins fixed</li>
|
||
<li>Labels on genomic alignments fixed</li>
|
||
<li>Upload data option from Tools menu fixed</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_17">Release Notes for MSA Viewer Version 1.8 (April 19, 2018)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_17">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Navigation toolbar improved with capabilities to project features </li>
|
||
<li>Implemented scrolling of alignments within the MSA Viewer dedicated area </li>
|
||
<li>Implemented new coloring for CDS alignments to show non-synonymous nucleotide codons (menu Coloring)</li>
|
||
<li>Tooltips usability improvement – tooltip popup logic made less aggressive</li>
|
||
<li>Improved scrolling/positioning to use smooth animation</li>
|
||
<li>Improved tooltip content to better explain consensus symbol and correctly show ambiguous consensus bases</li>
|
||
<li>Improved feature projection for alignment with local features</li>
|
||
<li>Improved accessibility (508) compliance</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_12">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed production crashes related to back-end OpenGL (MESA) initialization</li>
|
||
<li>Fixed incorrect column statistics in tooltips</li>
|
||
<li>Fixed issue with Organism name not being shown for some data</li>
|
||
<li>Fixed issues with setting Master sequence on some data sets</li>
|
||
<li>Fixed double appearance for tooltips</li>
|
||
<li>Fixed issue with ‘X’ character in protein alignments and ‘X’ in consensus</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_18">Release Notes for MSA Viewer Version 1.7 (December 28, 2017)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_18">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Added <a href="/tools/msaviewer/tutorial1/#panorama">navigation toolbar with pile-up graph with variation and coverage histogram</a></li>
|
||
<li>Added <a href="/tools/msaviewer/embedding-api/#parameters">API</a> to hide strand column for DNA alignments</li>
|
||
<li>Context (right-click) menu improved for usability</li>
|
||
<li>Major rendering engine upgrade to support large size alignments without limits on projected feature row expansions </li>
|
||
<li>Usability improvements to make alignments more readable: larger fonts, option not to display matching (consensus) letters, etc.</li>
|
||
<li>Improved performance of back-end consensus calculations</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_13">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed issue with incorrect URL parameters processing for the master/anchor row </li>
|
||
<li>Fixed front-end issues with unsetting default master/anchor row</li>
|
||
<li>Fixed bug with master not shown in the consensus=false mode</li>
|
||
<li>Fixed visual glitches with stand indicator, (+) button, etc.</li>
|
||
<li>Fixed some browser compatibility issues</li>
|
||
<li>Fixed issues with the ruler rendering and behavior</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_19">Release Notes for MSA Viewer Version 1.6 (June 27, 2017)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_19">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Switched to use Ext JS 6.5</li>
|
||
<li>Added ability to download alignment in FASTA format</li>
|
||
<li>Warning added for missing appname parameter</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_14">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed tool-tip information shifting for DNA alignment</li>
|
||
<li>Fixed tool-tip opening over menu</li>
|
||
<li>Fixed feedback link</li>
|
||
<li>Fixed wrong position of the tool-tip when scrolling the page</li>
|
||
<li>Fixed selection on event processing demo in Chrome and Firefox</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_20">Release Notes for MSA Viewer Version 1.5 (April 18, 2017)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_20">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Added status bar</li>
|
||
<li>Added context menu to provide links to Entrez to sequences in the alignment</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_15">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed issue with not showing species name for uploaded alignment</li>
|
||
<li>Fixed sudden back-end crash</li>
|
||
<li>Fixed issues with alignments based on local sequences</li>
|
||
<li>Fixed incorrect error handling in the back-end</li>
|
||
<li>Fixed various issues with the demo pages</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_21">Release Notes for MSA Viewer Version 1.4 (February 21, 2017)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_21">New Features and Improvements</h2>
|
||
|
||
|
||
<p>NONE</p>
|
||
|
||
|
||
<h2 id="bug-fixes_16">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed issue with blank space when zoomed in on some alignments from BLAST under condition, that the Master alignment is set</li>
|
||
<li>Fixed incorrect tooltip information</li>
|
||
<li>Fixed issues with showing FASTA alignments with gaps produced by MUSCLE</li>
|
||
<li>Fixed IE issues with Upload dialog</li>
|
||
<li>Fixed zooming problem when Master alignment is on the negative strand</li>
|
||
<li>Fixed issues with text import via clipboard paste</li>
|
||
<li>Fixed issues with text and labels renderings (scrambled unreadable text)</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_22">Release Notes for MSA Viewer Version 1.3 (January 23, 2017)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_22">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Implemented new coloration method “Conservation” (see <a href="/tools/msaviewer/embedding-api/#conservation">Embeddind API documentation</a> and <a href="/tools/msaviewer/tutorial1/#conservation">Getting Started tutorial</a> )</li>
|
||
<li>Improved tooltips to offer short or detailed mode based on users choice</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_17">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed issue with zoom and position loss when user changes the master sequence</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_23">Release Notes for MSA Viewer Version 1.2 (December 26, 2016)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_23">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Implemented support for NCBI COBALT results, RIDs from COBALT can be visualized now</li>
|
||
<li>Added CDD features projection</li>
|
||
<li>Improved <a href="/tools/msaviewer/tutorial1/#step4">selection of current coloring</a> in the menus</li>
|
||
<li>Added menu links to coloring scheme documentation</li>
|
||
<li>Improved tooltip timings for appearance and decay</li>
|
||
<li>Added the <a href="https://www.youtube.com/watch?v=NZ1vsIp0j_8&feature=youtu.be">Introducing Multiple Sequence Alignment Viewer</a> video tutorial</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_18">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed critical issue on touch screen enabled devices</li>
|
||
<li>Fixed insertion appearance for BLAST alignments with no master</li>
|
||
<li>Fixed issues with the ruler length when new master row is picked</li>
|
||
<li>Fixed conflicts with context menu and tooltips in IE and Safari browsers</li>
|
||
<li>Fixed issue with image drift on color scheme change</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_24">Release Notes for MSA Viewer Version 1.1 (September 27, 2016)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_24">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>New improved rendering mechanism for displaying projected features</li>
|
||
<li>Improved navigation over gaps in alignments</li>
|
||
<li>Improved security and compatibility with HTTPs protocols</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_19">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed number of navigation issues, related to zoom levels</li>
|
||
<li>Fixed issues with organism names for some imported alignments</li>
|
||
<li>Fixed issues with not showing features on protein alignments</li>
|
||
<li>Fixed various tooltip issues</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_25">Release Notes for MSA Viewer Version 1.0 (June 27, 2016)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_25">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Implemented loading of FASTA Text Alignments (compatibility with MUSCLE and similar tools)</li>
|
||
<li>Implemented various <a href="/tools/msaviewer/embedding-api/#setcoloring">alignments colorings/scores</a></li>
|
||
<li>Implemented <a href="/tools/msaviewer/embedding-api/#including">API to embed Multiple Sequence Alignments View on your page</a></li>
|
||
<li>Implemented <a href="/projects/msaviewer/demo_mapping.html">API for alignment coordinate transformation</a></li>
|
||
<li>Improved tooltips to be less aggressive</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_20">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Fixed number of browser compatibility issues</li>
|
||
</ul>
|
||
|
||
|
||
<h1 id="release-notes-for-msa-viewer-ver_26">Release Notes for MSA Viewer Version 0.1 (May 24, 2016)</h1>
|
||
|
||
|
||
<h2 id="new-features-and-improvements_26">New Features and Improvements</h2>
|
||
|
||
|
||
<ul>
|
||
<li>Multiple Sequence Alignment Viewer is a new product which shows multiple alignments in a Web view</li>
|
||
<li>It can be embedded in your page by using <a href="/tools/msaviewer/embedding-api/">Embedding API</a></li>
|
||
<li>It supports several data formats: NCBI ASN.1 alignment and Genome Workbench Project, MUSCLE (FASTA alignment) is being implemented</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="bug-fixes_21">Bug Fixes</h2>
|
||
|
||
|
||
<ul>
|
||
<li>As this is the pilot version there are no bugs identified yet</li>
|
||
</ul>
|
||
|
||
|
||
</div>
|
||
<!--/.col1-->
|
||
<div class="col2">
|
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<h2 id="table-of-contents">Table of Contents</h2><ul>
|
||
<li><a href="/projects/msaviewer/">Multiple Sequence Alignment Viewer application</a></li>
|
||
<li><a href="/tools/msaviewer/">Documentation home</a></li>
|
||
<li>General<ul>
|
||
<li><a href="/tools/msaviewer/about/">About</a></li>
|
||
<li><a href="/tools/msaviewer/embedding-api/">MSA Viewer Embedding API</a></li>
|
||
<li><a href="/tools/msaviewer/release-notes/">Release Notes</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Help<ul>
|
||
<li><a href="/tools/msaviewer/tutorial1">Guide to Using the MSA Viewer</a></li>
|
||
<li><a href="/tools/msaviewer/video/">Video Tutorials</a></li>
|
||
<li><a href="/tools/msaviewer/legend/">Legend</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Demo Pages<ul>
|
||
<li><a href="/projects/msaviewer/demo/demo_static.html">Static embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_dynamic.html">Dynamic embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_sort.html">Sorting parameters embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_consensus.html">Consensus parameters embedding</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_events.html">Event Handling</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_coloring.html">Coloring</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_columns.html">Customizing Columns</a></li>
|
||
<li><a href="/projects/msaviewer/demo/demo_mapping.html">Alignment Coordinate Transformation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Related Resources<ul>
|
||
<li><a href="/projects/sviewer/">Sequence Viewer</a></li>
|
||
<li><a href="/projects/treeview/">Tree Viewer</a></li>
|
||
</ul>
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