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Mrbayes and RAxML different phylogeny

I am working on construction of phylogeny based on Mrbayes and RAxML. I used the Prottest to get the best model for ML (FLU+I+G+F) and BIC (FLU+G+F). I tried FLU for RAxML,but when I used RAxML I could not find the FLU model, so instead i used the prset aamodelpr=fixed(mix) parameter and the third ranked model from ProtTest(GTT+G+F) with preset aamodelpr= fix(jone). But the results are totally different from RAxML results, which is completely not what i expected. So can anyone give me some suggestion? As the results showed the most significant bias is that one of my specials owns longer branch than its closest species.

alignment
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updated by Ram Ram • written by xinwangcau • xinwangcau

2 answers

This is a comprehensive presentation about Mrbayes and RAxML common features and differences.

http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf

It's from 2010, there probably were some changes and upgrades, but main features have hopefully remained the same.

To see other discussions look at the reference below.

https://www.google.ru/?gfe_rd=cr&ei=H58CV-b9F8vFZNyMqAg&gws_rd=ssl#newwindow=1&q=Mrbayes+and+RAxML+different+phylogeny

To see scientific conclusions you can ask your question at NCBI web-site: www.ncbi.nlm.nih.gov

The result is the following:

http://www.ncbi.nlm.nih.gov/pmc/?term=Mrbayes%20and%20RAxML%20different%20phylogeny

Look at this paper, for example:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221724/

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

RAxML runs for several weeks sometimes, but FastTree is really fast and does not loose

a lot of other positive features of RAxML.

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written by natasha.sernova natasha.sernova

Thank you for the answer.BTW do you know any information about the model of FLU in Mrbayes? I wanna to construct the phylogeny based on the best-fit model, but could not find in the Mrbayes.

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written by xinwangcau • xinwangcau

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