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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
---------------------------------------------------------------------
1. Installing D-Tailor
1.1. Prerequisites
D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.
D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).
To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
- UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
- RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
- TransTermHP — http://transterm.cbcb.umd.edu/
All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 1.2. Installation
D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.
1.3. License
D-Tailor is licensed under the BSD 2-Clause License.
2. D-Tailor tutorial
For detailed documentation please see tutorial/dtailor_tutorial.PDF

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