- // NeighborJoiningF foresterClustering = NeighborJoiningF
- // .createInstance();
- // aptxTree = foresterClustering.execute(distances);
+
+ for (SequenceI sequence : sequences)
+ {
+ Sequence seq = ForesterConversions
+ .createForesterSequence(sequence, true);
+ PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
+ NodeData nodeData = sequenceNode.getNodeData();
+ nodeData.setSequence(seq);
+
+ nodesBoundAlignment.put(sequenceNode, sequence);
+ alignmentBoundNodes.put(sequence, sequenceNode);
+ rootNode.addAsChild(sequenceNode);
+ }