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I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the tag would consist of two different values: 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 an alignment. Based on the aligned data we need a phylogenetic tree. The software then 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 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 shows what we want to achieve. Every node should get a tag. In the shown case, it could also be possible that all nodes would get a second tag of 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 has already developed a software which fits our needs for the alignment and the phylogenetic tree, using the Biopython package.

The question is: is there already a software (preferably open source) which does everything that we want — align imported data and create a phylogenetic tree and tag and export data? Or do we need to improve our own software by adding the ability to tag?

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

Edit:

The text above mainly explains what we have. How we implemented everything with Biopython isn't relevant to this question. I only posted it 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 a software which can align data, create a phylogenetic tree, add user-defined tags, and export the data, we would prefer to use this software instead of modifying our own.

As a possible hint, the software MEGA (http://www.megasoftware.net/) can align data and create a phylogenetic tree, but it doesn't allow for editing/adding tags.

I hope this question is now clearer.

In case you want to know, the algorithm we used to create the phylogenetic tree was Maximum Likelihood

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    $\begingroup$ It's not clear what you're searching for. Please clearly lay out what Biopython doesn't do that you still want to do. Please also be aware that questions regarding analytical methods, such as those related to bioinformatics or biological simulation, that do not ask explicitly about the underlying biology are considered off-topic. Please edit your post to address only your question relating to biology or delete it and visit another Stack Exchange site such as Stack Overflow for programming, Cross Validated for statistics, etc. You may also find Biostars helpful. $\endgroup$ – MattDMo Oct 27 '16 at 12:49
  • $\begingroup$ In case you might be interested, here are some python-based tools that include tree manipulation functions: etetoolkit.org p4.nhm.ac.uk $\endgroup$ – bli Oct 28 '16 at 12:13

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