Visualising a subset of the tree of life
http://phylot.biobyte.de/ performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables). 

For example, the input of tree elements


  Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia
  radiculosa,Paramecium tetraurelia,Tetrahymena
  thermophila,Cryptosporidium muris,Cryptosporidium hominis,Blastocystis
  hominis


generates the tree