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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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output methods text and suggested citations #29

Closed roblanf closed 8 years ago

roblanf commented 9 years ago

Following a conversation on twitter, we realised it might be helpful to output at the end of any given run the suggested citations and methods text. This could incorporate:

  1. Suggested citations
  2. Citations in bibtex format
  3. Suggested text

All of these would be determined by the details of the analysis someone ran. E.g. did it use PhyML, RAxML, or something else? Did it use algorithms (like the relaxed clustering or kmeans) described in other publications? Which version of PF did it use?

E.g. if some ran relaxed clustering in PF2, that would use RAxML, the relaxed clustering algorithm, and PF2, so the text might read:

"To determine an appropriate partitioning scheme, we used the relaxed clustering algorithm [ref1] implemented in PartitionFinder 2.0 [ref2], which relies on RAxML [ref3]".

And then the refs in text and possibly bibtex format.

roblanf commented 9 years ago

NB: this should be printed to stdout as part of the general output, and also added to a section at the end of the best_scheme.txt file.

roblanf commented 8 years ago

done.