Newbie has 2 questions about rooting and dating a tree

[bonisko]

Dear all,

I recently installed IQ-tree v 2.3.4 for Windows. I have executed Iqtree2 with a Clustal alignment of 98 sequences which gives a tree that is very similar to the output of Mega11.

Next I created a calibration file with dates for 3 nodes. IQtree completed with no errors. I opened the output file (nwk) which I can root, but the nodes I used to calibrate are REALLY different than what I specified in my DateFile. (Eg. 2 Gya vs 370 Mya!)

Any idea what I am doing wrong?

In Mega, I must root a tree before dating, but I see no way to do this in IQtree. Might this be my problem?

Thanks to anyone with an idea!

Bruce
Berkeley CA

[roblanf]

Hi @bonisko,

In order to help you, we'll need more information. Can you provide the full command line, input and output files? Also just tagging @tothuhien since this is partly a dating question.

Rob

[bonisko]

Thanks! 13 files zipped and attached.
Bruce

iqtree2 -s AtpBNoSpacesClustal.fas -T AUTO --date DATE_FILE.txt

13Files_for_Rob.zip

[bonisko]

Oops. Forgot to tag @tothuhien

Thanks!

Bruce

[tothuhien]

Hi,
Very sorry for the delay! I'm just back from my holiday so was not aware of this. I see in the command line that you haven't specified the date for the tips. I assumed they are all 0, so could you try again by adding option --date-tip 0 ?
Hien

[roblanf]

Edited this from --date-tips to --date-tip as corrected by @tothuhien, just so I can mark it as the answer.

[bonisko]

Hi Hien,

Thanks! But this gives an error, although the syntax looks correct. (See http://www.iqtree.org/doc/iqtree-doc.pdf)

C:/Invalid "--date-tips" option. And I am sure I am passing a zero, not the letter O.

Ideas?

Bruce

[tothuhien]

Hi, sorry the option is --date-tip and not --date-tips, could you try again?
Hien

[bonisko]

Problem solved!

Thanks!

Bruce