How to prepare sequences for recombination analysis?

PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program

GNU General Public License v3.0

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How to prepare sequences for recombination analysis? #63

Closed NailouZhang closed 1 year ago

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 sequences for recombination analysis?

NailouZhang commented 1 year ago

I took some inspiration from the RDP5 manual. I believe I can solve this problem.

NailouZhang commented 1 year ago

http://web.cbio.uct.ac.za/~darren/RDP5Manual.pdf