diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index 714e55b09b..e3abbea6bd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -153,7 +153,7 @@ public void setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNAS
 	}
 
 	private DNASequence getRawParentSequence(String accessId) throws IOException {
-		String seqUrlTemplate = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text";
+		String seqUrlTemplate = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text";
 		URL url = new URL(String.format(seqUrlTemplate, accessId));
 
 		logger.trace("Getting parent DNA sequence from URL: {}", url.toString());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
index 46d058ec0f..8f1b449283 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -57,7 +57,7 @@
  * </ul>
  *
  * Taken from <a
- * href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"
+ * href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"
  * >NCBI</a> with slight modification and put into the classpath resource.
  *
  * Takes in an ID, name, amino acid string and the locations of amino acids
@@ -65,7 +65,7 @@
  * position strings that correspond to the amino acid string or if you are using
  * the default IUPAC codes you can use the hardcoded ones which are consistent
  * amongst all <a
- * href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"> codon
+ * href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"> codon
  * tables</a>.
  *
  * The generated {@link IUPACTable} objects do not parse the data further until
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 24b5ce1ada..045900263a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -56,7 +56,7 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 
 	private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
 
-	private static final String eutilBaseURL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
+	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
 	private String genbankDirectoryCache = null;
 	private GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
 	private GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml b/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
index 47e75cafd9..a1e441c505 100644
--- a/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastn</BlastOutput_program>
   <BlastOutput_version>BLASTN 2.2.29+</BlastOutput_version>
diff --git a/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java b/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
index e36d728ace..8684ba1257 100644
--- a/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
+++ b/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
@@ -28,6 +28,7 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.secstruc.DSSPParser;
+import org.biojava.nbio.structure.secstruc.SecStrucCalc;
 import org.biojava.nbio.structure.secstruc.SecStrucInfo;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
 
@@ -61,19 +62,26 @@ public static void main(String[] args) throws IOException,
 
 		// Print the Author's assignment (from PDB file)
 		System.out.println("Author's assignment: ");
-		List<SecStrucInfo> ssi = SecStrucTools.getSecStrucInfo(s);
-		for (SecStrucInfo ss : ssi) {
-			System.out.println(ss.getGroup().getChain().getName() + " "
-					+ ss.getGroup().getResidueNumber() + " "
-					+ ss.getGroup().getPDBName() + " -> " + ss.toString());
-		}
+		printSecStruc(s);
 
 		// If the more detailed DSSP prediction is required call this
 		DSSPParser.fetch(pdbID, s, true);
 
 		// Print the assignment residue by residue
 		System.out.println("DSSP assignment: ");
-		ssi = SecStrucTools.getSecStrucInfo(s);
+		printSecStruc(s);
+
+		// finally use BioJava's built in DSSP-like secondary structure assigner
+		SecStrucCalc secStrucCalc = new SecStrucCalc();
+
+		// calculate and assign
+		secStrucCalc.calculate(s,true);
+		printSecStruc(s);
+
+	}
+
+	public static void printSecStruc(Structure s){
+		List<SecStrucInfo> ssi = SecStrucTools.getSecStrucInfo(s);
 		for (SecStrucInfo ss : ssi) {
 			System.out.println(ss.getGroup().getChain().getName() + " "
 					+ ss.getGroup().getResidueNumber() + " "
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index 717d429eee..f4d76c7df8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
index ad9dd1615d..6a5aa6dc93 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
index 3379895038..b4d6479620 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
index 62a5735d16..d6fc87a506 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
index a89500596c..51c51f8c17 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index 368e03a805..a82b9ac67d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
index 8e276afa0a..ca38425aa9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
index 60e5a05c33..5f940ec6a1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
index 08a81eebb4..74c6d66ce5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
index e8546908f8..b4200cd88f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
index 8e9dd2e8f9..cb5ae3628b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
index 351d531d07..d111e55fd6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index dedeaabad8..2908f91e42 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
index ba3de809f6..1cc883145f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
@@ -34,7 +34,7 @@
  * chain, residue ranges and status (manual or automatic classification).
  * <p>
  * For detailed explanation about the ECOD information see the original article
- * at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
+ * at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
  * <pre>
  * Cheng H, Schaeffer RD, Liao Y, et al. 
  * ECOD: An Evolutionary Classification of Protein Domains. 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 749b2bbcd3..e2d1efd6ab 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -67,6 +67,17 @@ public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
 		return listSSI;
 	}
 
+
+	public static void assignSecStruc( Structure s,List<SecStrucInfo> listSSI){
+
+		for ( SecStrucInfo ssi : listSSI){
+
+			ssi.getGroup().setProperty(Group.SEC_STRUC,ssi);
+
+		}
+
+	}
+
 	/**
 	 * Obtain the List of secondary structure elements (SecStrucElement) of a
 	 * Structure.
diff --git a/biojava-structure/src/main/resources/ce.properties b/biojava-structure/src/main/resources/ce.properties
index 769c77ac18..d3016afc3d 100644
--- a/biojava-structure/src/main/resources/ce.properties
+++ b/biojava-structure/src/main/resources/ce.properties
@@ -11,14 +11,14 @@ ce.about=<h1>Protein Structure Comparison Tool V ${project.version}</h1> \
       Prli&#263; A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE.<br>\
       Pre-calculated protein structure alignments at the RCSB PDB website<br>\
       Bioinformatics (2010) 26 (23): 2983-2985<br>\
-      [<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/20937596\">PubMed</a>]<\
+      [<a href=\"https://www.ncbi.nlm.nih.gov/pubmed/20937596\">PubMed</a>]<\
       [<a href=\"http://bioinformatics.oxfordjournals.org/content/26/23/2983.full.pdf\">pdf</a>]<br>\
       <hr>\
       <b>CE Reference:</b><br>\
       Shindyalov IN, Bourne PE (1998)<br>\
 	  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.<br>\
       Protein Eng 11: 739-747<br>\
-	  [<a href="http://www.ncbi.nlm.nih.gov/pubmed/9796821">PubMed</a>]\
+	  [<a href="https://www.ncbi.nlm.nih.gov/pubmed/9796821">PubMed</a>]\
 	  [<a href="http://peds.oxfordjournals.org/cgi/reprint/11/9/739">pdf</a>]<br>\
 	  <hr>\
  	  <b>FATCAT Reference:</b><br>\
@@ -35,7 +35,7 @@ ce.about=<h1>Protein Structure Comparison Tool V ${project.version}</h1> \
       BioJava: an open-source framework for bioinformatics in 2012<br>\
       Bioinformatics (2012) 28 (20): 2693-2695<br>\
       [<a href=\"http://www.biojava.org\">BioJava website</a>]\
-      [<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/22877863\">PubMed</a>]\
+      [<a href=\"https://www.ncbi.nlm.nih.gov/pubmed/22877863\">PubMed</a>]\
       <hr>\
       <b>Jmol web site:</b>\
       <a href=\"http://www.jmol.org\">http://www.jmol.org</a>\
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
index 4c70b8147f..061475071a 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
@@ -27,7 +27,7 @@
  * Alignment request parameters accepted by QBlast service.<br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
  * <p/>
- * Taken from <a href=http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
+ * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
  */
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
index d0dc973f38..dfa144864d 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
@@ -27,7 +27,7 @@
  * Output parameters accepted by QBlast service. <br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
  * <p/>
- * Taken from <a href=http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
+ * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
  */
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 2e4c47cbdd..3d9ad05377 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -208,7 +208,7 @@ public int getBlastWordSize() {
 	 * <b>WARNING!!</b> At this point, the method does not verify the validity of your choice; for example, word size of
 	 * greater than 5 with blastp returns error messages from QBlast. Word size range depends on the algorithm chosen.
 	 * <p>
-	 * More at http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html
+	 * More at https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html
 	 * <p>
 	 * Blastall equivalent: -W
 	 *
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
index 12538465bf..a57d0170dd 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -64,9 +64,9 @@ public class NCBIQBlastService implements RemotePairwiseAlignmentService {
 	public static final long WAIT_INCREMENT = 3000;
 
 	private static final MapToStringTransformer MAP_TO_STRING_TRANSFORMER = new MapToStringTransformer();
-	private static final String SERVICE_URL = "http://blast.ncbi.nlm.nih.gov/Blast.cgi";
+	private static final String SERVICE_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
 	private static final String DEFAULT_EMAIL = "anonymous@biojava.org";
-	private static final String DEFAULT_TOOL = "biojava3";
+	private static final String DEFAULT_TOOL = "biojava5";
 
 	private URL serviceUrl;
 	private String email = DEFAULT_EMAIL;
diff --git a/readme.md b/readme.md
index 4efff1d54c..79b4b04182 100644
--- a/readme.md
+++ b/readme.md
@@ -72,4 +72,4 @@ This list is intended for more technical discussions about API design, bugs in g
 **BioJava: an open-source framework for bioinformatics in 2012**<br/>
 *Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
 [Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
+[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](https://www.ncbi.nlm.nih.gov/pubmed/22877863)