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Repository files navigation

SEDA licenserelease

SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.

SEDA Screenshot

Main features

Among other functions, SEDA allows you to:

  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.

Debugging

In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.

For programmers

Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.

Citing

Please, cite the following publication if you use SEDA:

  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI

Works using SEDA

  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI

Credits

The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.

About

SEquence DAtaset builder

www.sing-group.org/seda/

Topics

bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences

Resources

Readme
GPL-3.0 license
Activity
Custom properties

Stars

6 stars

Watchers

4 watching

Forks

2 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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" + '

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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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SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
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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); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
SEDA licenserelease
SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences. Please, visit the official web page of the project for downloads, a complete online manual and support.
SEDA Screenshot
Main features
Among other functions, SEDA allows you to:
  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Edit sequence headers in different ways.
  • Remove duplicated sequences.
  • Remove isoforms.
  • Sort, merge, split, or reformat FASTA files.
  • Use BLAST to perform different types of queries.
  • Use Clustal Omega to perform multiple sequence alignments.
  • Perform gene annotation using different tools: Splign/Compart, ProSplign/ProCompart, Augustus (as implemented in SAPP), or the Conserved Genome Annotation (CGA) Pipeline.
Debugging
In case you need see the commands executed by SEDA to run third-party software, just run SEDA with -Dseda.execution.showcommands=true.
For programmers
Programmers can take advantage of the SEDA core to develop new operations to process FASTA files. In addition, SEDA has a plugin-based architecture, so new functions can be added to SEDA through plugins. Take a look at the manual for detailed information about this.
Citing
Please, cite the following publication if you use SEDA:
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C. P. Vieira; J. Vieira (2022) SEDA: a Desktop Tool Suite for FASTA Files Processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 19(3), pp. 1850-1860. DOI
Works using SEDA
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) A bioinformatics protocol for quickly creating large-scale phylogenetic trees. 12th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2018. Toledo, Spain. 20 - June DOI
  • H. López-Fernández; P. Duque; S. Henriques; N. Vázquez; F. Fdez-Riverola; C.P. Vieira; M. Reboiro-Jato; J. Vieira (2018) Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences. Interdisciplinary Sciences: Computational Life SciencesDOI
  • H. López-Fernández; P. Duque; N. Vázquez; F. Fdez-Riverola; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2019) Inferring Positive Selection in Large Viral Datasets. 13th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2019. Ávila, Spain. 26 - June DOI
Credits
The Command-Line Interface (CLI) available from SEDA v1.6.0 was developed by David Vila Fernández as Master's Project.
About
SEquence DAtaset builder
www.sing-group.org/seda/
Topics
bioinformaticsfastafasta-sequencesjavasequence-dataset-buildersequences
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
6 stars
Watchers
4 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages