I have tried to construct a phylogenetic tree using BioJava code. The available code is here: TreeConstructor<proteinsequence, aminoacidcompound=""> treeConstructor = new TreeConstructor<>(msa, TreeType.NJ, TreeConstructionAlgorithm.PID, new ProgessListenerStub()); treeConstructor.process(); String newick = treeConstructor.getNewickString(true, true); System.out.println(newick); The output I get is this: (((((Haemophilus:15.22466516494751,Escherichia:15.750478267669678):9.353089968363443,Chlamydophi:29.174633344014488):0.9799249172210693,Treponema_p:28.513384103775024):0.9321229457855225,Helicobacte:28.39388108253479):13.432122111320496,Mycoplasma_:13.432122111320496); The newick string I get is fine and can be read from Treeview. The only problem is the names of the species are not complete. i.e Haemophilus_influenzae_Rd_KW20 is shrunk to Haemophilus and likewise for other species names. I have no idea why? I am 100% confident that the correct names are passed as parameters but when the newick string is generated, for some reason, the correct names are not displayed. Any help is welcome...