在 treeannotator 分析后得到负分支长度的原因可能是什么？
What can be the reason of getting negative branches lengths after treeannotator analysis?
我认为 BEAST 不允许在先验分布级别上出现负长度的分支，所以当我在 FigTree 中查看我的共识树时，我感到非常惊讶。
这可能是什么原因以及如何应对这种现象？
我正在分析大约 1500 个 HAV 分类群（亚型：IA，区域：VP1），下一个参数是：GTR+Γ、严格时钟、合并恒定种群。树是由 treeannotator 通过 ~/beast/bin/treeannotator -heights median -burnin 20 -limit 0.5 VP1_test_bt_ExpPop.trees VP1_test_bt_ExpPop.tree
生成的
我在 ResearchGate 上找到了来自圣地亚哥 Sanchez-Ramirez 的答案，让我在这里引用它：
Try using the option -heights ca when you run TreeAnnotator. This stands for "common ancestor trees" and aims at summarizing clade ages across all posterior trees and not only the values for subset of trees that have that clade. If that subset of trees is low in frequency the average node height might end up being older than the direct ancestor.
Here is the explanation for negative branches:
"MCC trees produced by TreeAnnotator can have a descendent node that is older than its direct ancestor (a negative branch length). This may seem like an error but is actually the correct behaviour. The MCC tree is, by default, generated with average node heights across all trees in the sample which contain that clade. The negative branch lengths result when a clade is at low frequency and tends not to occur in those trees that have the MCC tree's ancestral clade (or vice versa). This means the average heights are for the adjacent nodes are derived from different sets of trees and may not have any direct ancestor-descendent relationship."
In this paper you will find more information about the ca option: Looking for trees in the forest: Summary tree from posterior samples
我认为 BEAST 不允许在先验分布级别上出现负长度的分支，所以当我在 FigTree 中查看我的共识树时，我感到非常惊讶。
这可能是什么原因以及如何应对这种现象？
我正在分析大约 1500 个 HAV 分类群（亚型：IA，区域：VP1），下一个参数是：GTR+Γ、严格时钟、合并恒定种群。树是由 treeannotator 通过 ~/beast/bin/treeannotator -heights median -burnin 20 -limit 0.5 VP1_test_bt_ExpPop.trees VP1_test_bt_ExpPop.tree
我在 ResearchGate 上找到了来自圣地亚哥 Sanchez-Ramirez 的答案，让我在这里引用它：
Try using the option
-heights cawhen you run TreeAnnotator. This stands for "common ancestor trees" and aims at summarizing clade ages across all posterior trees and not only the values for subset of trees that have that clade. If that subset of trees is low in frequency the average node height might end up being older than the direct ancestor. Here is the explanation for negative branches: "MCC trees produced by TreeAnnotator can have a descendent node that is older than its direct ancestor (a negative branch length). This may seem like an error but is actually the correct behaviour. The MCC tree is, by default, generated with average node heights across all trees in the sample which contain that clade. The negative branch lengths result when a clade is at low frequency and tends not to occur in those trees that have the MCC tree's ancestral clade (or vice versa). This means the average heights are for the adjacent nodes are derived from different sets of trees and may not have any direct ancestor-descendent relationship." In this paper you will find more information about thecaoption: Looking for trees in the forest: Summary tree from posterior samples