Using a fixed local clock, relative rate or absolute rate?

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Hoss S

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Aug 14, 2025, 3:30:29 PMAug 14
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Hello BEAST community,
i am sorry if this is posted elsewhere, i can't find an answer to it anywhere. I have a set of sequences, and i'm using BEAST to do a host-specific local clock. There is a hostA and a hostB within my sequences. I defined a taxon set 'hostB' and i clicked the monophyletic option. I chose the fixed local clock option. I am using BEAST/BEAUTi 1.10.4. I set priors for hostB.rate and clock.rate based on my prior knowledge about their rates. 
i have about 250 hostA sequences and 39 hostB sequences. I have two questions:
1. is hostB.rate a relative rate or an absolute rate? if i want to get a distribution for the evolutionary rate, should i multiply with clock.rate or just use it as is?
2. i didn't set a separate monophyletic taxon set for hostA. i'm assuming clock.rate covers everything other than hostB. is this right?

Sorry if this a basic question! i am a bit new to this, not sure how to interpret my results. Your help would be appreciated!

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