🔍 Common Reasons Why the Cladogram Looks "Unnormal"

🧬 1. Poor Signal in the Data

• If your alignment has low variability (e.g., binary data with few informative sites), IQ-TREE may fail to fully resolve relationships.
• This results in collapsed nodes, polytomies, or zero-length branches.

✅ Solution: Check how many parsimony-informative sites are in your data. IQ-TREE logs this at the beginning of the run. If it's too low, the data may not be sufficient for a reliable tree.

⚙️ 2. Model or Data Type Mismatch

• Using the wrong model for your data type can distort the inference.
• Since you’re using binary data, the model JC2+FQ+ASC is appropriate — but only if the data: Is coded as 0/1 Has no constant (invariant) sites, or you use +ASC to correct for that

✅ Solution: Ensure you are using +ASC if you removed constant sites (which is common in binary data). If not, the likelihood will be biased, and the topology can be off.

🌳 3. Collapsed or Polytomous Tree

• IQ-TREE automatically collapses weakly supported branches, which can make the tree look "unnormal" (e.g., like a bush rather than a tree).
• The tree becomes non-binary (polytomous) if some splits can’t be confidently resolved.

✅ Solution: Use this option to avoid automatic collapsing:

iqtree2 -s input.phy -m JC2+FQ+ASC --polytomy NO

Also, add Bootstrap support:

-bb 1000 -alrt 1000

🖼️ 4. Misinterpreting the Tree Viewer Output

• Some viewers (like FigTree, Dendroscope, or iTOL) might not handle collapsed or multifurcating trees well.
• Sometimes labels are missing or internal nodes look like tips, making it appear "unnormal".

✅ Solution:

• Try viewing the tree in multiple programs (e.g., FigTree, iTOL).
• Check the .treefile and .log files — do the taxon names match your alignment?
• Avoid using extremely short taxon names or special characters.

🧾 5. Taxon Placement Issues

• If some taxa appear not at the tips, it usually means: They're incorrectly labeled They are midpoints in unrooted trees The tree is ladderized or improperly visualized

✅ Solution:

• Confirm taxon names in your alignment and tree match exactly.
• Try rerooting the tree for better visualization (-root option in iTOL or FigTree).
• In IQ-TREE, you can root manually using:iqtree2 -t yourtree.treefile -root "OutgroupTaxon"

🧪 Summary of Fixes

Problem Likely Cause Fix Polytomies or missing branches Weak support or data noise Add --polytomy NO and boost with -bb or -alrt Tips missing or misplaced Taxon name error or midpoint rooting Check name formatting and use correct rooting Strange topology Low-informative binary data Remove noise, use more informative sites Wrong model behavior No +ASC correction Always use +ASC for binary data with constant site removal

If you share your tree file (.treefile) or the alignment format (FASTA/PHYLIP), I can look at it and help diagnose exactly what's going on.

Dear Lu,

Anomalous topologies may result from factors such as incorrect evolutionary model selection, the absence of a defined outgroup, or inadequate MCMC sampling. I recommend using raxmlGUI as a reliable alternative for phylogenetic inference.