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chaoszhang / ASTER

Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
GNU Affero General Public License v3.0
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About parameter settings for caster-site #24

Closed NZY1314 closed 6 months ago

NZY1314 commented 6 months ago

Hi,

If I want to run 1000 bootstrap replicates for my SNP dataset, what parameter should I set? -R or -s?

Best wishes

NZY1314 commented 6 months ago

Hi,

I mean, is it should be like in the command line as ./caster-site -R 1000 -o 40_SNP_samples all.LDfilter.min4.phy? Or ./caster-site -s 1000 -o 40_SNP_samples all.LDfilter.min4.phy?

Best wishes,

chaoszhang commented 6 months ago

If you just want some Bootstrap supports, then caster-site will automatically computes local bootstrap supports based on 1000 replicates. However, there is no simple way to generate bootstrap trees.

NZY1314 commented 6 months ago

Ok, Thank you so much.