谱系速率多样化BAMM 分析 2025-03-29

RevBayes需要进一步的研究

使用BAMM估算分化速率
学习记录——BAMM计算多样化速率
BAMM 分析系统发生物种多样化率 入门学习

使用figtree输出Newick格式的树文件

R中操作

library(ape)
v <- read.tree("Test1-MCMCtree.tree")
is.ultrametric(v)
is.binary.tree(v)

v <- force.ultrametric(v)

write.tree(v, file="output-Test1-MCMCtree.tree")

# Now to check min branch length:
min(v$edge.length)

library(BAMMtools)
setBAMMpriors(v)
#bamm -c testcontrol.txt
#下载https://github.com/macroevolution/bamm
#https://www.bilibili.com/opus/939709655783833603
edata <- getEventData(tree, eventdata = "data/dragonflies_event_data.txt",
                      burnin = 0.1)
summary(edata)
plot.bammdata(edata, legend = TRUE, lwd = 2)