Host 35.193.113.52
United States
GOOGLE-CLOUD-PLATFORM
Ubuntu
Software information

nginx nginx 1.10.3

tcp/443 tcp/80

  • Open service 35.193.113.52:80 · phylocorrelate.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 301 Moved Permanently
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:25 GMT
Content-Type: text/html
Content-Length: 194
Connection: close
Location: https://phylocorrelate.uwaterloo.ca/

Page title: 301 Moved Permanently

<html>
<head><title>301 Moved Permanently</title></head>
<body bgcolor="white">
<center><h1>301 Moved Permanently</h1></center>
<hr><center>nginx/1.10.3 (Ubuntu)</center>
</body>
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  • Open service 35.193.113.52:443 · pathfams.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 200 OK
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:24 GMT
Content-Type: text/html; charset=UTF-8
Content-Length: 13439
Connection: close
X-Powered-By: Shiny Server
x-ua-compatible: IE=edge,chrome=1
Vary: Accept-Encoding

Page title: PathFams
    <div>
      <img src="logo2.png" height="53" width="50"/>
          
      <a id="HOMEPAGE" href="#" class="action-button" style="color:#000000">PathFams</a>
    </div>
  

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    <div>
      <img src="logo2.png" height="53" width="50"/>
       &nbsp;&nbsp; 
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<body>
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          <span class="navbar-brand">
            <div>
              <img src="logo2.png" height="53" width="50"/>
               &nbsp;&nbsp; 
              <a id="HOMEPAGE" href="#" class="action-button" style="color:#000000">PathFams</a>
            </div>
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            <a href="#tab-4495-7" data-toggle="tab" data-value="&lt;div&gt;&#10;  &lt;img src=&quot;logo2.png&quot; height=&quot;53&quot; width=&quot;0&quot;/&gt;&#10;  About&#10;&lt;/div&gt;">
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                About
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    <div class="container-fluid">
      <div class="tab-content" data-tabsetid="4495">
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  • Open service 35.193.113.52:80 · pathfams.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 301 Moved Permanently
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:24 GMT
Content-Type: text/html
Content-Length: 194
Connection: close
Location: https://pathfams.uwaterloo.ca/

Page title: 301 Moved Permanently

<html>
<head><title>301 Moved Permanently</title></head>
<body bgcolor="white">
<center><h1>301 Moved Permanently</h1></center>
<hr><center>nginx/1.10.3 (Ubuntu)</center>
</body>
</html>
    Found 2026-01-24 by HttpPlugin
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  • Open service 35.193.113.52:443 · phylocorrelate.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 200 OK
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:25 GMT
Content-Type: text/html; charset=UTF-8
Content-Length: 5801
Connection: close
X-Powered-By: Shiny Server
Accept-Ranges: bytes
Cache-Control: public, max-age=0
Last-Modified: Sat, 24 Apr 2021 14:22:42 GMT
ETag: W/"16a9-1790442e1fb"
Vary: Accept-Encoding

Page title: PhyloCorrelate Homepage

<!DOCTYPE html>
<html lang="en-US" xmlns="http://www.w3.org/1999/xhtml">
<head>
  <title>PhyloCorrelate Homepage</title>
  <style type="text/css">
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      margin: 0 auto .5em auto;
      padding: .2em;
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    }
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      margin-right: auto;
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      margin: 1em auto 1em auto;
      float: left;
    }
    #main{
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      line-height: 24px;
    }
    #inner {
      width:50%;
      margin: 0 auto;
      margin-right: 190px;
    }
    .button {
      background-color: #4ca64c;
      border: 3px solid black;
      color: white;
      padding: 15px 25px;
      text-align: center;
      font-size: 16px;
      cursor: pointer;
      border-radius: 30px;
    }
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      width: 100%;
      background-color: #FFF;
      color: grey;
      padding: 20px;
      width: 97%;
    }
  </style>
</head>
<body>
  <div id="titleBar">
    <div id="container">
      <h1>PhyloCorrelate</h1>
    </div>
  </div>
  <div id="outer-content">
    <div id="content">
      <div id="main">

        <h1>Overview</h1>

        <p>Phylocorrelate is a tool that detects pairs of gene/protein families with similar phylogenetic distributions across the bacterial tree of life. The database contains pre-computed phylogenomic correlations for 27,372 gene families across 28,315 species. PhyloCorrelate uses the GTDB bacterial tree and gene occurrences from AnnoTree including entries from KEGG, PFAM, and TIGRFAM.</p>

        <p>Gene co-occurrence is important to detect as it may suggest an interaction between the genes, membership in the same pathway or complex, or more general functional associations or dependencies.</p>

        <br>
        <div id="wrapper" style = "text-align: center;">
          <p><img src="./logo.png" height="126" width="180"></p>
        </div>

        <div id="wrapper" style = "text-align: center;">
          <a href="./app/"><button class="button" style="width:180px;"><b>Launch</b></button></a>
        </div>

        <div id="inner">
          <p style="width:400px;text-align:justify;">Explore phylogenomic correlations for existing genes/proteins of interest, or submit new genes for co-occurrence analysis.</p>
        </div>

          <br></br>

          <h1>How does it work?</h1>

          <p>PhyloCorrelate detects pairs of gene/protein families with similar phylogenetic distributions across the bacterial tree of life. To find genes with similar distributions to a query gene (e.g., cobD below), first we examine the presence/absence distribution of the query gene across the tree. We then examine the distributions of all other genes and calculate their similarity using several metrics, including the Jaccard overlap coefficient (JC) and hypergeometric p-value statistic. The genes with the highest JC scores will be the top candidate correlation partners.</p>

          <p>But it isn’t quite so simple. PhyloCorrelate also implements a phylogenetic correction to ensure that co-occurrence patterns are statistically significant given the topology of the tree. This helps to remove apparent correlations that occur only because gene A and B happen to be conserve
    Found 2026-01-24 by HttpPlugin
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  • Open service 35.193.113.52:80 · diffbase.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 301 Moved Permanently
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:25 GMT
Content-Type: text/html
Content-Length: 194
Connection: close
Location: https://diffbase.uwaterloo.ca/

Page title: 301 Moved Permanently

<html>
<head><title>301 Moved Permanently</title></head>
<body bgcolor="white">
<center><h1>301 Moved Permanently</h1></center>
<hr><center>nginx/1.10.3 (Ubuntu)</center>
</body>
</html>
    Found 2026-01-24 by HttpPlugin
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  • Open service 35.193.113.52:443 · diffbase.uwaterloo.ca

    2026-01-24 03:47 

    HTTP/1.1 200 OK
Server: nginx/1.10.3 (Ubuntu)
Date: Sat, 24 Jan 2026 03:47:25 GMT
Content-Type: text/html; charset=UTF-8
Content-Length: 3922
Connection: close
X-Powered-By: Shiny Server
Accept-Ranges: bytes
Cache-Control: public, max-age=0
Last-Modified: Sun, 10 Jan 2021 14:08:23 GMT
ETag: W/"f52-176eca06598"
Vary: Accept-Encoding

Page title: DiffBase

<!DOCTYPE html>
<html lang="en-US" xmlns="http://www.w3.org/1999/xhtml">
<head>
  <title>DiffBase</title>
  <style type="text/css">
    body, html {
      font-family: Helvetica, Arial, sans-serif;
      background-color: #F5F5F5;
      color: #114;
      margin: 0;
      padding: 0;
    }
    a {
      text-decoration: none;
    }
    a:hover {
      text-decoration: underline;
    }
    #titleBar {
      height: 80px;
      background-color: #FFF;
      overflow: hidden;
      border-bottom: 1px solid #d3d3d3;
    }
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      margin-top: 14px;
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      margin: 0 auto .5em auto;
      padding: .2em;
      color: #D9230F;
      text-align: center;
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      max-width: 910px;
      margin-left: auto;
      margin-right: auto;
    }
    #content {
      margin: 1em auto 1em auto;
      margin-bottom: 150px;
      float: left;
    }
    #main{
      float: left;
      line-height: 24px;
    }
    .button {
      background-color: #D9230F;
      border: none;
      color: white;
      padding: 15px 25px;
      text-align: center;
      font-size: 16px;
      cursor: pointer;
      border-radius: 10px;
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      background-color: grey;
    }
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      background-color: #FFF;
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      left: 0;
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      background-color: #FFF;
      color: grey;
      padding: 20px;
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  </style>
</head>
<body>
  <div id="titleBar">
    <div id="container">
      <h1>DiffBase: A bioinformatic classification of <i>C. difficile</i> toxins</h1>
    </div>
  </div>
  <div id="outer-content">
    <div id="content">
      <div id="main">

        <br>
        <div id="wrapper" style = "text-align: center;">
          <a href="./app-A/"><button class="button">Toxin A</button></a>
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          <a href="./app-B/"><button class="button">Toxin B</button></a>
        </div>

        <br>
        <br>
        <div id="wrapper" style = "text-align: center;">
          <a href="./straintable.html"><button class="button">Strain table</button></a>
        </div>

        <br>
        <br>

        <div class="boxed">
          <h2 align = "center">Description</h2>
          <p>DiffBase is an online database of Toxin A (TcdA) and Toxin B (TcdB) protein sequences derived from currently available <i>C. difficile</i> strains. TcdA and TcdB have been bioinformatically classified into distinct groups (subtypes) based on their sequence similarities. The full bioinformatic analysis pipeline is described here: <a href="https://github.com/doxeylab/diffbase">github.com/doxeylab/diffbase</a>.</p>

          <h2 align = "center">Citation</h2>
          <p>Mansfield, M.J., Tremblay, B.J.M., Zeng, J., Wei, X., Hodgins, H., Worley, J., Bry, L., Dong, M., and Doxey, A.C. (2020). Phylogenomics of 8,839 <em>Clostridioides difficile</em> genomes reveals recombination-driven evolution and diversification of toxin A and B. PLOS Pathogens 16(12): e1009181. <a href="https://doi.org/10.1371/journal.ppat.1009181">https://doi.org/10.1371/journal.ppat.1009181</a>.</p>

          <h2 align = "center">Funding</h2>
          <p>This project was funded by NSERC. <img src="./NSERC.jpg" height="27" width="60"/></p>

        </div>

      </div>
    </div>
  </div>
  <div class="footer">
    <p style="text-align:left;">
      Benjamin Tremblay - Software/database development
      <span style="float: right;">
        Min Dong - Project supervision
      </span>
    </p>
    <p style="text-align:left;">
      Michael Mansfield - Data analysis
      <span style="float: right;">
        Andrew Doxey - Project supervision
      </span>
    </p>
  </div>
</body>
</html>
    Found 2026-01-24 by HttpPlugin
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diffbase.uwaterloo.capathfams.uwaterloo.caphylocorrelate.uwaterloo.ca
Fingerprint:
c93204d7c94d708fa99e02ef813969db16beb6cc8848aee6225f1968a6baa929
CN:
diffbase.uwaterloo.ca
Key:
RSA-2048
Issuer:
R12
Not before:
2026-01-24 02:47
Not after:
2026-04-24 02:47
Domain summary

phylocorrelate.uwaterloo.ca 1 pathfams.uwaterloo.ca 1 diffbase.uwaterloo.ca 1

3 recorded

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