I´m doing bayesian trees with molecular markers to study parasites populations. I would like to make a tree with nodes with posterior probability greater than 0.5 so that it can be shown on a paper. I run the BEAST software and it runs perfectly. Then I set in TreeAnnotator a posterior probability limit on 0.5. But when I use Figtree to visualize the tree, it shows me all the nodes, even them with very low probabilities. How can I hide them?
Can someone help me please?
Maybe you could try this online tool: https://itol.embl.de/
There's an option to do this in Dendroscope iirc http://dendroscope.org/
Hi there,
It usually depends on the software you use for the graphic representation of your tree. If you use FigTree there is an option to eliminate all the values from the nodes under a certain threshold. I think it should be under the "Node labels" menu.
Hope this helps!
You need to remember that posterior probabilities are *probabilities* not statistical support percentages like bootstrap and jackknife. So, with bayesian analyses you need to be cautious about giving any weight to PP values less than 0.95
Lucas no se si ya solucionaste este tema con las recomendaciones de arriba. En mi opinión, una buena opción es darle a TreeAnnotator el arbol sobre el que querés anotar esas PP. Es decir calculá el árbol consenso de mayoría 50 (lo podes hacer con TNT o APE de R) y se lo das como árbol target a TreeAnnotator.
Ahí el soft va a calcular las PPs en base ese árbol y vas a tener en los nodos solo PPs mayores o iguales a 0.5.
Saludos.
Thank you all for collaborating with your responses. They have been very helpful!
Buenísimo Alfredo Holley , voy a probar con eso. Gracias!
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