alrt + ufboot error

[Rohit-Rannavre]

Hello there,

I am expecting SH-like alrt and bootstrap support values but getting a weird output from the following command:

iqtree3.exe -s PrimatesAligned.phy -m MFP -B 1000 -merit BIC -alrt 1000 -mtree -T AUTO -pre result -redo

Output in "result.treefile":

(Tarsius_syrichta:0.4217529729,Lemur_catta:0.2833645543,((((((Homo_sapiens:0.0486973467,Pan:0.0593196613)99.5/99.5/93.7/95.5/99.2/90.6/91.8/99.6/85.9/99.6/90.6/99.6/99.6/99.6/92.6/92/98.6/92.3/92/90:0.0234027930,Gorilla:0.0590827170)92.2/98.5/99.7/99.8/95.9/99.8/99.8/99.7/99.8/99.8/99.8/99.8/99.7/99.7/99.7/99.2/90.3/99.3/99.1/100:0.0675570027,Pongo:0.1338871352)94.7/95.8/98.1/99.2/90.5/99.3/99.4/99.2/99.2/93.4/99.3/99.4/95.3/93.5/95/94.5/99.3/90.9/92.6/92:0.0442845924,Hylobates:0.1619698266)91.4/89.9/99.3/92.7/99.8/95.9/96/95.3/95.5/95.9/95.9/91.8/99.2/99/98.1/99.6/99.5/93.9/98.1/99:0.0985338027,Macaca_fuscata:0.2699621871)98.3/94.3/90.8/99.7/99.6/93/99.6/90/92.7/90.5/93/92/93.4/74/99.2/98.2/95.8/99.7/95.3/96:0.1129768271,Saimiri_sciureus:0.3882884842)99.2/99.3/91.6/85.9/93.4/99.6/92.1/93.5/99.7/99.2/99.6/96.1/90/94/91.7/91.7/94.1/98.1/99.3/99:0.2152058036);

Hope you solve this issue. Thanks.

[bqminh]

Thanks for the report. It's already happening in IQ-TREE 2, when combining -alrt and -mtree option. While doing ModelFinder, it's still doing SH-aLRT test, and thus assigning support values onto the trees for each model during model testing. The values you see are SH-aLRT associated with all models that were being tested.

The workaround for now is to remove -alrt. When the run finishes, you can assign aLRT supports onto the final tree like:

iqtree3.exe -s PrimatesAligned.phy -m BEST_MODEL_FROM_1ST_RUN -alrt 1000 -T AUTO -te result.treefile -pre result2