tempest

[sehrish kakakhel]

hi beast users, I am trying to run tempest. it give me blue and red highlighted sequences. whether I have to remove only blue sequences or red one also? kindly guide me  

[Guillem Mas]

Hi,

to my extend, the color in the tree will just mean if the branches are upon or below the inferred regression. To better inspect which sequences that may be problematic and may need to be removed, I would rather take a look at the `Residuals' panel in TempEst and select the points which are appear far away from the central distribution. Keeping those data points selected in the `Residuals', you can then navigate back to the 'Tree'  panel and see which are the names an location of the problematic taxons that may be removed. You can find in this work from Baele et al., a nice tutorial on setting up such TempEst analysis.

Best,

Guillem

Missatge de sehrish kakakhel <sayyar...@gmail.com> del dia dc., 10 de març 2021 a les 9:37:

hi beast users, I am trying to run tempest. it give me blue and red highlighted sequences. whether I have to remove only blue sequences or red one also? kindly guide me  

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[Anna Kovalenko]

super! Thank you Guillem!

ср, 10 мар. 2021 г. в 19:06, Guillem Mas <guillem....@gmail.com>:

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[sehrish kakakhel]

thankyou Guillem. In my data, the value of R2 and correlation coefficient is 5.5E-3. Does it mean there are no temporal signals ??? kindly guide me.

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[guillem....@gmail.com]

Yes, this very low value does not fit into a clock-like behavior suitable for Bayesian inference. Perhaps you may try methods based on Maximum-likelihood (TreeeTime or LSD2)

Guillem

El dia dijous, 11 de març de 2021 a les 6:42:29 UTC+1, sayyar...@gmail.com va escriure: