User: robert.zimmermann

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Posts by robert.zimmermann

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Comment: C: Will lowering the LengthTol parameter increase false positive links in Orthology
... Dear Adrian, Thanks much for your comment! That's quite helpful. In fact, we are only interested in HOGs as we are using OMA as a quick way to determine gene gains, losses and duplications of a subset of genes of interest in all 5 taxa we are investigating. Note that Brachyury is a gene (also kn ...
written 13 months ago by robert.zimmermann10
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Will lowering the LengthTol parameter increase false positive links in Orthology Groups?
... We noticed that a key gene to our study was not placed considered in any orthology group for our OMA standalone run owing to the fact that it is a transcription factor (Brachyury) and has a shorter conserved domain. By testing on a small subset it seems like lowering the LengthTol parameter to 0.4 a ...
orthologs oma written 13 months ago by robert.zimmermann10 • updated 13 months ago by david_emms40
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Answer: A: Pysam under pypy?
... Because this problem comes up quite frequently for me, I reimplemented a lot of the pysam functionality in python code so it could be run with pypy. Feel free to fork it and clean it up. https://github.com/nijibabulu/pypysam/ ...
written 2.3 years ago by robert.zimmermann10

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