phyloP or PhastCons

[Avro1986]

Hi everyone,

I am looking at phylogeny between 9 plant genomes. I want to look at the conservation of certain elements. I know phyloP and PhastCons are useful tools. However, which one would you recommend? Some people told me that phyloP is good at computing conservation for individual bases whereas PhastCons is good for multibase alignments. However, when reading phyloP documentation, I can compute p-values for entire segments. I am a bit confused.

Any help would be greatly appreciated.

Thank you!

[Jane M]

Hello,

I know a bit both tools, so I cannot answer specifically to your answer. But when reading your topic, I just wonder why don't you keep positions that are predicted conserved by one of the tools? (since both have advantages).
Did you check if they give a lot of different results?