Skip to content

Commit 37eaaec

Browse files
lafitalafita
committed
Use HSDM substitution matrix instead of BLOSUM45 in MSA trees
1 parent 77379f0 commit 37eaaec

2 files changed

Lines changed: 12 additions & 14 deletions

File tree

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java‎

Lines changed: 6 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -78,8 +78,7 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
7878
private JCheckBox colorByBlocks;
7979
private List<JCheckBox> selectedStructures;
8080

81-
private static final String LIGAND_DISPLAY_SCRIPT =
82-
"select ligand; wireframe 40; spacefill 120; color CPK;";
81+
private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
8382

8483
private static final Logger logger = LoggerFactory
8584
.getLogger(MultipleAlignmentJmol.class);
@@ -414,13 +413,12 @@ public void actionPerformed(ActionEvent ae) {
414413
// Kimura, Structural and Fractional Dissimilarity Score
415414
Phylogeny kimura = MultipleAlignmentTools
416415
.getKimuraTree(multAln);
417-
Phylogeny blosum = MultipleAlignmentTools
418-
.getBLOSUM40Tree(multAln);
419-
Phylogeny structural = MultipleAlignmentTools
420-
.getStructuralTree(multAln);
416+
Phylogeny hsdm = MultipleAlignmentTools.getHSDMTree(multAln);
417+
// Phylogeny structural = MultipleAlignmentTools
418+
// .getStructuralTree(multAln);
421419

422-
Archaeopteryx.createApplication(new Phylogeny[] { kimura,
423-
blosum, structural });
420+
Archaeopteryx
421+
.createApplication(new Phylogeny[] { kimura, hsdm });
424422
}
425423
} catch (Exception e) {
426424
logger.error("Could not complete display option.", e);

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -867,25 +867,25 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
867867

868868
/**
869869
* Calculate a phylogenetic tree of the MultipleAlignment using
870-
* dissimilarity scores (DS), based in BLOSUM40 Substitution Matrix (ideal
871-
* for distantly related proteins, often the case in structural alignments)
872-
* and the Neighbor Joining algorithm from forester.
870+
* dissimilarity scores (DS), based in HSDM Substitution Matrix (ideal for
871+
* distantly related proteins, structure-derived) and the Neighbor Joining
872+
* algorithm from forester.
873873
*
874874
* @param msta
875875
* MultipleAlignment of protein structures
876876
* @return Phylogeny phylogenetic tree
877877
* @throws CompoundNotFoundException
878878
* @throws IOException
879879
*/
880-
public static Phylogeny getBLOSUM40Tree(MultipleAlignment msta)
880+
public static Phylogeny getHSDMTree(MultipleAlignment msta)
881881
throws CompoundNotFoundException, IOException {
882882
MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = MultipleAlignmentTools
883883
.toProteinMSA(msta);
884884
BasicSymmetricalDistanceMatrix distmat = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
885-
.dissimilarityScore(msa, SubstitutionMatrixHelper.getBlosum40());
885+
.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000102"));
886886
Phylogeny tree = TreeConstructor.distanceTree(distmat,
887887
TreeConstructorType.NJ);
888-
tree.setName("BLOSUM40 Tree");
888+
tree.setName("HSDM Tree");
889889
return tree;
890890
}
891891

0 commit comments

Comments
 (0)