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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
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OpenRDP run slow, Can I speed it up? #62

Closed NailouZhang closed 1 year ago

NailouZhang commented 1 year ago

Hi,

When I ran OpenRDP with my sequence (72 taxa and 10,999 sites), it ran for a long time. Can I speed it up?

ArtPoon commented 1 year ago

Currently your best option for speed is to run the original RDP. We are working on improving and optimizing OpenRDP, but this effort is not supported by any research grants, so progress will be slow without help from the community.

NailouZhang commented 1 year ago

Thank you, It's a great work. I prefer to run bioinformatical analysis in the command line. I wish I could do something to help with this work, but it is difficult for me. I'm so sorry.

ArtPoon commented 1 year ago

Thanks! Bioinformatics is all about the CLI. Maybe sometime in the near future you might be able to pitch in :-)

NailouZhang commented 1 year ago

Hi, Are there ways to speed up recombination analysis, such as by setting nucleotide identity thresholds to reduce the number of sequences, or by cutting for highly variable regions?

Before recombination analysis, I tried to remove replicated sequences with cd-hit, then filter columns with trimAl. However, I don't think that these are the right things. Can you give some tips on how to prepare for a recombination analysis?