For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea.  LocTree2 has performed on par with or better than any other state-of-the-art method.  The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. 
LocTree2
LocTree3 prediction of localization.The prediction of protein sub-cellular localization is an important step toward elucidating protein function.  Here, we report the availability of LocTree3 as a public web server.  Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18=80±3% for eukaryotes and a six-state accuracy Q6=89±4% for bacteria.  The web server is available at http://www.rostlab.org/services/loctree3.
LocTree3