Ручное построение

http://forum.molgen.org/index.php?topic=518.10;wap2

Дискуссии на тему ДНК-генеалогии > Филогения и кладистика

Ручное построение дерева (wertner)

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Vadim Verenich
MrBayes -Программа для анализа филогений с помощью байезовской инференции.  Понимает формат Nexus.
Я конвертнул поправленный Вадимом У. ych файл в формат nex (отдельное спасибо Саше Лифанову за конвертер), немножко поправил файл согласно примерам, и запустил марковскую цепочку по методу Монте-Карло. Работает нормально, но медленно - на 145 гаплотипов примерно 3500 циклов за 20 минут.

Вадим, что вы думаете по этому поводу? 

http://mrbayes.csit.fsu.edu/wiki/index.php/Tutorial#When_to_Stop_the_Analysis

wertner
Цитата: Vadim Verenich от 06 Сентября 2009, 23:25:00>>>>MrBayes -Программа для анализа филогений с помощью байезовской инференции.  Понимает формат Nexus.
Я конвертнул поправленный Вадимом У. ych файл в формат nex (отдельное спасибо Саше Лифанову за конвертер), немножко поправил файл согласно примерам, и запустил марковскую цепочку по методу Монте-Карло. Работает нормально, но медленно - на 145 гаплотипов примерно 3500 циклов за 20 минут.

Вадим, что вы думаете по этому поводу? 

http://mrbayes.csit.fsu.edu/wiki/index.php/Tutorial#When_to_Stop_the_Analysis
<<<<Очень интересно! Буду разбираться.

Vadim Verenich
На выходе после "прожига" деревьев генерирует деревья в формате Newick. Good.

Цитировать>>>>The program will output a cladogram with the posterior probabilities for each split and a phylogram with mean branch lengths. The trees will also be printed to a file that can be read by tree drawing programs such as TreeView, MacClade, and Mesquite.<<<<
Quick Start Version

There are four steps to a typical Bayesian phylogenetic analysis using MrBayes:
Read the Nexus data file
Set the evolutionary model
Run the analysis
Summarize the samples
In more detail, each of these steps is performed as described in the following paragraphs.
1. At the MrBayes > prompt, type execute primates.nex. This will bring the data into the program. The data file (primates.nex) must be in the same directory as the MrBayes program. If you run into problems, refer to section 2.2 for possible solutions. If you are running your own data file, beware that it may contain some MrBayes commands that can change the behavior of the program; delete those commands or put them in square brackets to follow this tutorial.
2. At the MrBayes > prompt, type lset nst=6 rates=invgamma. This sets the evolutionary model to the GTR model with gamma-distributed rate variation across sites and a proportion of invariable sites. If your data are not DNA or RNA, if you want to invoke a different model, or if you want to use non-default priors, refer to the rest of this manual, particularly sections 3 to 5 and the Appendix.
3.1. At the MrBayes > prompt, type mcmc ngen=10000 samplefreq=10. This will ensure that you get at least 1,000 samples from the posterior probability distribution. For larger data sets you probably want to run the analysis longer and sample less frequently (the default sampling frequency is every 100th generation). You can find the predicted remaining time to completion of the analysis in the last column printed to screen.
3.2. If the standard deviation of split frequencies is below 0.01 after 100,000 generations, stop the run by answering no when the program asks "Continue the analysis? (yes/no)". Otherwise, keep adding generations until the value falls below 0.01.
4.1. Summarize the parameter values by typing sump burnin=250 (or whatever value corresponds to 25 % of your samples). The program will output a table with summaries of the samples of the substitution model parameters, including the mean, mode, and 95 % credibility interval of each parameter. Make sure that the potential scale reduction factor (PSRF) is reasonably close to 1.0 for all parameters; if not, you need to run the analysis longer.
4.2. Summarize the trees by typing sumt burnin=250 (or whatever value corresponds to 25 % of your samples). The program will output a cladogram with the posterior probabilities for each split and a phylogram with mean branch lengths. The trees will also be printed to a file that can be read by tree drawing programs such as TreeView, MacClade, and Mesquite.
It does not have to be more complicated than this; however, as you get more proficient you will probably want to know more about what is happening behind the scenes. The rest of this section explains each of the steps in more detail and introduces you to all the implicit assumptions you are making and the machinery that MrBayes uses in order to perform your analysis.

Vadim Verenich
Результаты пилотного запуска

Vadim Verenich
И кладограмма одного из 2001 вероятностных "деревьев"  (расчитанно в MrBayes, визуализированно в Mesquite)

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