what is the difference between .contree and .treefile? which one should I choose?

[Guoqing Li]

what is the difference between .contree and .treefile? which one should I choose? when i draw ml tree.

[Heiko Schmidt]

Dear Guoqing,

Thank you for your interest in IQ-Tree.

> what is the difference between .contree and .treefile? which one should I choose? when i draw ml tree.

If you do an ML-search including ultrafast-bootstrapping, than both files are created.

The treefile contains the best tree found by ML with the UFboot support values added.
The contree-file contains the consensus tree constructed from all UFboot trees (with the respective UFboot support values).

Thus, you get both files. (You find more details also in the documentation.)

Best regards,
Heiko Schmidt


-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5)
A-1030 Vienna, Austria
-----------------------------------------------------------------------------
Email: heiko.schmidt(AT)univie.ac.at
Tel. : ++43 +1 / 4277 - 74321
http://www.cibiv.at/
-----------------------------------------------------------------------------

[Jonathan Goodson]

I wanted to ask a followup question to this. In an analysis using only ultrafast bootstrap in addition to standard tree search, the .contree file includes a single integer support number that is apparently the percentage support from UFBoot. The .treefile file on the other hand includes more than a single number. It instead appears to have two different numbers, one of which is a 0-1.0 decimal value while the other, separated by a forward-slash, is an integer value. From comparison it appears that the second, integer, value corresponds to the values in the consensus tree file. What are the additional decimal values present in the ML tree file? It is not mentioned in the narrative description in the .iqtree output file or in the documentation as far as I can tell.

[Minh Bui]

Hi Jonathan, Can you please paste the command line used? Then we may be able to answer your question.

Cheers,

Minh

-- 
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/d5df5ee8-083b-4ea8-960d-b1523a9848d1%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jonathan Goodson]

I used the following, with different names for the input alignment, tree, and output prefix. Perhaps this is related to the use of an input tree?

iqtree -m LG+R10 -s input.faln -t input.nwk -nt 2 -bb 1000 -nm 25000 -pre output

In the .iqtree output the first (ML) tree notes:

Numbers in parentheses are  ultrafast bootstrap support (%)

but the support values look like 

(0.999/98)

(0.824/14)

(0.149/100)

On the second tree output (consensus) it describes them the same way, but the support values look like

(98)

(14)

(100)

The Newick output for the first tree contains support values like )0.999/98: while in the second, consensus tree they look like )98:

Thank you for your help,

Jonathan

Minh

To unsubscribe from this group and stop receiving emails from it, send an email to iqt...@googlegroups.com.

[Minh Bui]

Hi Jonathan,

Yes, these values were taken from the tree file input.nwk. IQ-TREE was trying to preserve those values for nodes that occur in both input tree and the final ML tree. So that’s a feature.

Cheers,

Minh

To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.

To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.

To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/96c292eb-25d7-473e-830e-c03d5d4f674f%40googlegroups.com.

[Wannes Dermauw]

Hi

I have a similar question re .contree and .treefile (created using the following command: iqtree -s infile.txt -bb 1000 -bnni -alrt 1000 -bcor 0.99 -st AA -m LG+I+G4+F -pre output -nt AUTO)

Only the .treefile contains both the SH-aLRT values and UF bootstrap values, while .contree contains UF bootstrap values only.

Is it possible to transfer the SH-aLRT values to the . contree file, for those splits that are identical?

If not, which tree should I use for further analyis/consider as the final tree: the best ML tree (.treefile) or the consensus tree?

Thank you very much in advance!

Wannes

Op woensdag 3 juli 2019 01:30:21 UTC+2 schreef Minh Bui:

Minh

To unsubscribe from this group and stop receiving emails from it, send an email to iqt...@googlegroups.com.

To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.

[Minh Bui]

Hi Wannes,

The point why IQ-TREE doesn’t compute SH-aLRT on the contree (consensus tree) is because this tree might be multifurcating, and this test only works on strictly bifurcating trees. 

However if the contree is indeed bifurcating, then you can do a 2nd run to compute SH-aLRT values on this tree with -te option, e.g.:

iqtree -s infile.txt -te CONTREE_FILE -alrt 1000 -m LG+I+G4+F -pre alrt_output -nt AUTO

Note here that these support values are now appended after the UFBoot values.

Cheers

Minh

To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/d949552a-14f2-40f1-a490-b30355948d9c%40googlegroups.com.

[Wannes Dermauw]

Hi Minh Bui

Thank you for the clarification. THat worked!

Op woensdag 6 mei 2020 03:26:48 UTC+2 schreef Minh Bui:

To unsubscribe from this group and stop receiving emails from it, send an email to iqt...@googlegroups.com.