tree topology test: docs don't match help options?

[xvazquezc]

Hi,

I just wanted to report a discrepancy that I've seen for a while in IQ-TREE I thought it'd be fixed in v3 but it's still there.

I'm not sure if I'm missing anything but the documentation for the tree topology tests, doesn't match the iqtree -h output. This mainly applies to the flags/options (none of them match!).

This is in the docs:

This is the printed help in the command line:

TREE TOPOLOGY TEST:
  --trees FILE         Set of trees to evaluate log-likelihoods
  --test NUM           Replicates for topology test
  --test-weight        Perform weighted KH and SH tests
  --test-au            Approximately unbiased (AU) test (Shimodaira 2002)
  --au-epsilon NUM     Epsilon for AU test: if |deltaL| < NUM, keep tree regardless of p-value (default: 0.001)
  --sitelh             Write site log-likelihoods to .sitelh file

Cheers,
Xabi

[bqminh]

Thanks for pointing out this inconsistency. Since a few years now IQ-TREE introduces new double-dash options, but still keep the short form for compatibility.

• --trees is equivalent to -z
• --test is equivalent to -zb
• --test-weight is equivalent to -zw
• --test-au is equivalent to -au
• --au-epsilon is a new option (since 12 Mar 2026) to address a bug AU test returns significant p-value when log-likelihood difference is zero or near-zero (rare bug) #138
• --sitelh is equivalent to -wsl

Free feel to update the document and I will review your pull request. As for how, see https://github.com/iqtree/iqtree.github.io