Hello,   
I'm working for a software company and for one of our project's we need a software to cluster nodes in a phylogenetic tree which have a certain kind of similarity and give them a user defined tag. Preferable the tag consist of two different value's, a unique ID and a human readable name. It would also be nice to set multiple tags for one or several nodes.   


Some more in depth information:   
We get sequenced data from a laboratory. The first thing the software has to do, is to do an alignment. Based on the aligned data we need a phylogenetic tree. The software now has to give us the possibility to set one or more tags on one or more nodes. After the tagging, the data has to be exported from the software, so that we can give our clients the enriched data.  

Phylogenetic tree:   

                                            ________ M.HpyFI.dna
                                            |
                                            |_______________ M2.HpyFXIII.dna
                                            |
                                            |___________ M.HpyFII.dna
                                            |
                                            |        ___ M.HpyFIII.dna
                                            |_______|
                                            |       |__________ M.HpyFIV.dna
                                            |
                                            |  ________________ M.HpyFVII.dna
                                            |_|
                                            | |__________ M.HpyFXII.dna
      ______________________________________|
                                            |____________ M.HpyFIX.dna
                                            |
                                            |    ________ M.HpyFVI.dna
                                            |___|
                                            |   |_________ M.HpyFVIII.dna
                                            |
                                            |_____________ M.HpyFORFX.dna
                                            |
                                            |   _________ M.HpyFV.dna
                                            |__|
                                            |  |____________ M.HpyFXI.dna
                                            |
                                            |____ M1.HpyFXIII.dna



Phylogenetic tree with tags:  
(This graphic just shows what we want to achieve. Every node should get a tag. In the shown case it could also be possible that all nodes get a second tag called citrobacter.)        

                     ________ M.HpyFI.dna
                    |
                    |_______________ M2.HpyFXIII.dna
                    |
                    |___________ M.HpyFII.dna
                    |
                    |        ___ M.HpyFIII.dna
                    |_______|
                    |       |__________ M.HpyFIV.dna
                    |
                    |  ________________ M.HpyFVII.dna
                    |_|
                    | |__________ M.HpyFXII.dna
     _______________|
                    |____________ M.HpyFIX.dna
                    |
                    |    ________ M.HpyFVI.dna (Citrobacter koseri)
                    |___|
                    |   |_________ M.HpyFVIII.dna (Citrobacter koseri)
                    |
                    |_____________ M.HpyFORFX.dna (Citrobacter koseri)
                    |
                    |   _________ M.HpyFV.dna (Citrobacter freundii)
                    |__|
                    |  |____________ M.HpyFXI.dna (Citrobacter freundii)
                    |
                    |____ M1.HpyFXIII.dna (Citrobacter freundii)



Our company already developed a software for the alignment and the phylogenetic tree which fits our needs with the Biopython package. The question is, if there is already a software (preferable open source) which does everything that we want or if we have to improve our own software.   

I hope it is clear what we want to achieve and what we are searching for. 

**Edit:**

The text above shows what we have. How we implemented everything with Biopython doesn't have any relevance to this question. I posted it only to show our workflow. 
At the moment our software is not able to place user defined tags as shown in the second phylogenetic tree. It is no problem for us to improve our software so that it can do the tagging. But if there exists already a software which can align data, create a phylogenetic tree an can add user defined tags + the export, we would preferably use this software than our software.
As a hint the software MEGA (http://www.megasoftware.net/) can align data and create a phylogenetic tree, but it is not possible to edit/add tags.

I hope the question is now clearer

*In case you want to know which algorithm we used to create the phylogenetic tree: Maximum Likelihood* 
take a look at the new ETE3 features ( http://mbe.oxfordjournals.org/content/33/6/1635 ).
You can either generate phylogenies using predefined workflows or edit existing trees to add as many labels as you need. Then export as extended newick, or tree images. The [Python AP][1]I should integrate well with your biopython pipeline.
hope it helps

  [1]: http://etetoolkit.org/