I want to run an analysis and have to use XML-based file format which I have never done before. The guide tree and the sequences have to be in the same file. Does anybody know a program which can generate such files easily?
Dear Peter,
If I correctly understood your question, BEAST would allow you to create XML file, but you have first to generate a nexus file based on your sequences and proceed with BEAUTI.
Good luck!
If this analysis you have to run is BEAST, than just download the whole BEAST package including BEAST, BEAUTi, Tracer, Tree Annotator etc. you will need all the aforementioned programmes to create your final tree.
You design the XML file with BEAUTi, run it with BEAST, check the runs with Tracer and create the final Tree with Tree Annotator.
Thanks for the info. Its not BEAST pack what I have to run, some other program which requires the XML format. I did the file this time by manual editing as I had not to many taxa. But I'm just wondering what if I have hundreds of taxa in my list?
Some R packages for phylogenetic analyses would have this functionality. For example: http://www.phytools.org/static.help/export.as.xml.html
I'm a quite new user, but I got this done using "beastgen" :
- download here: https://github.com/beast-dev/beast-mcmc#other-downloads
- some documentation here: http://beast.community/beastgen
However, maybe you are using BEAST2, and BEASTGen is part of BEAST v1. It's however compatible with the right template. It even works smoothly using an input fasta file. My template for the alignment part was:
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