I have 278 nucleotide sequences of a pest species. I am trying to build an ML phylogenetic tree by BEAST using CIPRES portal. I have converted fasta file into .xml using BEAUti. Then I used that .xml file in CIPRES to get output files using BEAST version 1.10.4 in XSDE. In output files, I m not getting .tre file, which is used in Tree Annotator for tree building. I tried many times but failed. Is there any detailed demo from the begining of sequence alignment to phylogenetic tree building? I hope someone could show me the detailed protocol of building ML phylogenetic tree by BEAST(1.10.4) on XSEDE on cipres.
Hi Tabasum Akhter
BEAST output will be give you Bayesian posterior probabilities not the Maximum likelihood Bootstrap values.
You can easily use one of these following programs in CIPRES:
- RAxML-HPC BlackBox (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping on XSEDE.
- RAxML-HPC2 on XSEDE (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
- RAxML-HPC2 Workflow on XSEDE (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
- RAxML-HPC v.8 on XSEDE (8.2.12) - NEW Interface! Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
- If there is any more question please don't hesitate to ask,
- Regards
Hi Tabasum Akhter,
BEAST is based on Bayesian algorithm but not Maximum likelihood (ML). You may use RaxML to reconstruct ML phylogenetic tree on CIPRES. Alternatively, you can use W-IQ-TREE, a fast online phylogenetic tool for maximum likelihood analysis. For more details, please visit: http://iqtree.cibiv.univie.ac.at/
All the best,
Fangluan
Thank you Fangluan Gao and Atena Eslami for your response. Actually I got wrong in my question. I need to get Bayesian phylogenetic tree, not ML, in CIPRES. I got my nucleotide fasta file convert to .xml, then used that file in CIPRES portal using BEAST 1.10.4, to get output file. I need .tre file as one of my output file, but I fail many times .I don't know if something is wrong in my input file or is there some other issue. It would be very useful if anybody can give me detailed demo from sequence alignment to Bayesian phylogenetic tree building using CIPRES.
Thanking. and help is highly appreciated.
First of all, please tell me how you change the FASTA to XML format.
This is a real important stage.
Then, you must set the BEAST toolkit in CIPRES.
Please write here your email address, then, I can send you the details.
Good luck,
Thanks a lot sir. I am sharing this information as.
I have set of 278 nucleotide sequences. First I convert fasta file into nexus format in MEGA 7.0. Then I use nexus file in BEAUti 1.10.4. Following parameters were set as.
1) In taxa, a new was added and all seqs. were added in included taxa.
2) In sites, substitution model is HKY, base frequencies is empirical and site heterogeneity is gamma.
3) In clock, its uncorrelated relaxed clock.
4) In trees, speciation is Yule process
5) In priors, distribution is normal
6) In MCMA, length of chain is 80,000, screen state is 200 and log parameter is 10000.
Sir, please mail me at [email protected]
If you want to use Mr Bayes to run Bayesian approach, then you must change FASTA to nexus!
For BEAST you must load the FASTA to Beauti .
Before loading your dataset, please use JModel test to find the best model for you data.
Hi Tabasum,
Please share you question/errors with beast-user group via:
https://groups.google.com/forum/#!forum/beast-users
if you explain the problem correctly you will receive useful feedback.
Thank you everyone for sharing useful comments. I have got output files from CIPRES using BEAST. I need to get .tre file(or .mcc file) which is needed in Fig Tree software to get Bayesian phylogenetic tree. But I am failing to get that file again and again. I am getting all other files (including .tree file, .log file etc) but not .tre file. Here I am attaching STDOUT file. I hope it helps to find out about the problem.
Thanks again all.
Please check it in dendroscope too. If still there is no image, I assume that your settings in CIPRES is not correctly arranged.
@Hamid Moazzen sir, I have got both .log and .tree files, but not .tre file in CIPRES. I doubt If I am doing something wrong while generating .xml file in BEAUti.
I have 270 sequences of mitochondrial COI from one species. I created fasta file, converted to nexus format and then into .xml in BEAUti. Parameters which I used are,
1) Sites, substitution model HYK, Base frequencies and Site Heterogeneity model as Gamma.
2) Clock type is Strict type
3) Tree Prior is Coalescent constant
4) Priors are normal
5) MCMC, length of chain 80,00,000, state screen 200 and log parameters 10000.
Tabasum Akhter if you have .tree file to need to use tree annotator to " summarize the information from a sample of trees produced by BEAST onto a single “target” tree " . please see https://beast.community/treeannotator
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