c***y
发帖数: 615 | 1 我读RAxML manual，只有inference啊，能具体解释下如何用RAxML计算吗？
多谢了！ |
|
x****6
发帖数: 4339 | 2
The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province
of China was first reported on December 30, 2019 by the Wuhan Municipal
Health Commission (WHO, 2020). The pneumonia cases were found to be linked
to a large seafood and animal market in Wuhan, and measures for sanitation
and disinfection were taken swiftly by the local government agency. The
Centers for Disease Control and Prevention (CDC) and Chinese health
authorities later determined and announced that a novel coro... 阅读全帖 |
|
H*g
发帖数: 2333 | 3 The public CIPRES parallel computation server also has built-in MUSCLE and
others that you could manually adjust the alignment parameters. It also
have
some downstream phylogenetic analysis tool, such as RaxML and MrBayes. I
personally find it very helpful.
If I were u,for the computation power, |
|
H*g
发帖数: 2333 | 4 For the convergence of Bayesian Inference tree, you could go to the .log
file, check the value behind the last "Average standard deviation of split
frequencies:". Without the info of this value at least, we would not know if
we have set the generation number or the probe temperature correctly, not
saying the resulted tree is appropriate for downstream analysis.
A good and biological meaningful alignment is essential for the analysis.
Make sure of this before jumping into the actual analysis. Thi... 阅读全帖 |
|
t*****z
发帖数: 1598 | 5 我用过Bio Linux，感觉没啥必要，就是个基于Ubuntu的定制版，而且还是基于过时的
Ubuntu版本。现在Ubuntu官方软件库里的生物类软件已经很丰富了。我是做进化分析的
，安装完Ubuntu要做的一件事情是：
sudo apt-get install phylip emboss jemboss jalview seaview clustalw clustalo
mafft t-coffee raxml phyml figtree fasttree mrbayes beast-mcmc
libhmsbeagle1
to |
|
c***y
发帖数: 615 | 6 一组数据一个是RAxML做的ML tree, 一个是fast tree 做的approximated ML tree. 相
比较下有多大区别？
多谢了！ |
|
|
t*****z
发帖数: 1598 | 8 你没法知道哪个树好，因为你不知道进化的真相是什么，除非你用的是模拟数据而非真
实数据。
除了RF距离，可以考虑用Consel做一下拓扑学假设检验。你得事先有可以用拓扑表示的
假设（例如：人跟猴子近而不是跟老鼠近），然后用RAxML基于这些假设（固定的拓扑
限制）建树，然后看似然值的差异，并计算显著性。Consel自动化了一些常见检验。 |
|
