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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
128 stars 33 forks source link

which tree should be used #38

Closed fujch7 closed 4 years ago

fujch7 commented 4 years ago

Thank you for developing the amazing tool.

After I run it, which output file should I use? And why the raxml_bestree_final.tre didn't show branch value?

Thanks very much!

fasnicar commented 4 years ago

Hi, many thanks for using PhyloPhlAn.

The output phylogeny might depend on the configuration file you used. From your message I can understand you used RAxML to reconstruct the phylogenetic tree. So, in this case, the RAxML_bestTree.*.tre is the output file. It is strange that there are no branch values though. can you provide the parameters you used in the configuration file for RAxML?

Many thanks, Francesco

fujch7 commented 4 years ago

run command： nohup phylophlan -i /home/0811/ --accurate --diversity medium -d phylophlan -f supermatrix_aa.cfg -t a --nproc 2 --output_folder /home/phy_output & configuration file is supermatrix_aa.cfg

The outputfile contains raxml_besttree.0811_refine.tre, raxml_info.0811_refine.tre, raxml_log.0811_refine.tre, raxml_result.0811_refine.tre, 0811.tre, 0811_resolved.tre.

0811.tre showed branch values but raxml_besttree.0811_refine.tre didn't.

Thanks very much!

fasnicar commented 4 years ago

Thanks, those are the defaults so it is strange that there are no branch lengths. Can you please send the raxml_besttree.0811_refine.tre file?

fujch7 commented 4 years ago

RAxML_bestTree.0811_refined.zip

fasnicar commented 4 years ago

Many thanks for the file. I correctly see the branch lengths in the file and it appears correctly visualized also from Archaeopteryx.

Capture

fujch7 commented 4 years ago
fasnicar commented 4 years ago

Ah! No problem. The default config files do not perform the bootstrap analysis, you can add it by manually edit the configuration file and adding to the RAxML params the bootstrap parameters. Alternatively, you can run just RAxML with the bootstrap params using the MSA that you can find in the output folder.

fujch7 commented 4 years ago

Thank you so much. Is it recommended to use the tree file input_folder.tre built by FastTree？

fasnicar commented 4 years ago

It depends on your configuration file, with the standard one the analysis generates first a quick tree using FastTree and then refines it using RAxML. So, with these settings you should wait for RAxML to complete the tree reconstruction. In any case, you can look at the FastTree tree to have a quick idea about the results.

Here it is briefly described the output files.

fujch7 commented 4 years ago

Ah! No problem. The default config files do not perform the bootstrap analysis, you can add it by manually edit the configuration file and adding to the RAxML params the bootstrap parameters. Alternatively, you can run just RAxML with the bootstrap params using the MSA that you can find in the output folder.

Could I use concanated concatenated.alnfile for just run RAxML-ng？

fasnicar commented 4 years ago

Yes, of course. The concatenated.aln file is provided by PhyloPhlAn as output to be used for other downstream analyses, like testing/comparing a different/alternative phylogeny reconstruction tool.