LSD2: Trouble with Branch Collapsing in IQ-TREE: Seeking Clarification on -l Option

[YangZhuoya]

I am currently using IQ-TREE version 2.3.2 for phylogenetic analysis and encountering an issue where a significant number of internal branches are automatically collapsed despite setting extremely low branch length thresholds. The error messages suggest using the -l option to set branch lengths, but this option appears to be invalid. I tried other versions and none of them works. Does someone know if the -l option is available or how can I generate binary tree without branch collapsing?

[roblanf]

Hi @YangZhuoya,

Can you post your commandline and the output file with the collapsed branches?

Thanks,

Rob

[YangZhuoya]

Hi Rob,

Thank you for your response. Below is the command line I used in IQ-TREE:

iqtree -s CA_S450L_300.fasta -keep-ident -m GTR+F+G4 --date CA_S450L_date.txt -fconst 758047,1449684,1444318,757918

And here is the output log file CA_S450L_300.fasta.log.

It said "Collapse 110 (over 297) internal branches having branch length <= 1.13e-07 (settable via option -l)". I look forward to any insights you might have on preventing these branches from collapsing. Thanks!

Zhuoya

[bqminh]

Please check if this thread in google group answers your question:
https://groups.google.com/g/iqtree/c/KVJ9Tx7YvRE/m/Lu4Gkpy-AAAJ
If not, please ask the author of LSD2 directly: https://github.com/tothuhien/lsd2. IQ-TREE merely uses LSD2 for tree dating.

[YangZhuoya]

Hi Rob
I found the solutions. Thanks so much!
Best,
Zhuoya

[tothuhien]

Hi Zhuoya,
I just answered the same question here:
#189
So briefly, if you want of force LSD2 not to make polytomies, for example you want the minimum branch length is 0.001, you can add the option:
--date-options "-l 0 -u 0.001"
Cheers,
Hien

[YangZhuoya]

Hi hien,
Problem solved! Thanks so much for the help!
Best,
Zhuoya