Constraint not compatible with ModelFinder?

[alephreish]

It seems that constraint is not taken taken into account if the model is not specified explicitly:

$ iqtree2 --version
IQ-TREE multicore version 2.3.0 COVID-edition for Linux 64-bit built Mar 14 2024
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
$ cat constr.tree 
((Human,Cow),(Seal,Whale));
#
# unconstrained
$ iqtree2 -s $CONDA_PREFIX/example.phy --prefix example.unconstr
# constrained, explicit model
$ iqtree2 -s $CONDA_PREFIX/example.phy -m TIM2+I+G -g constr.tree --prefix example.constr
# constrained, ModelFinder
$ iqtree2 -s $CONDA_PREFIX/example.phy -g constr.tree --prefix example.constr.auto
$ grep constraint example.*.log
example.constr.auto.log:Reading constraint tree constr.tree...
example.constr.auto.log:WARNING: Rooted constraint tree will be treated as unrooted tree
example.constr.log:Reading constraint tree constr.tree...
example.constr.log:WARNING: Rooted constraint tree will be treated as unrooted tree
#
# The constraint+ModelFinder tree is not different from the unconstrained tree:
$ nw_labels constr.tree | xargs nw_prune -v example.unconstr.treefile | nw_display - -w 60
                                      /--------------+ Human
                                      |                     
=-------------------------------------+ /-------+ Seal      
                                      | |                   
                                      \-+  /------+ Cow     
                                        \--+                
                                           \--------+ Whale 
                                                            
 |---------------|---------------|---------------|----      
 0             0.2             0.4             0.6          
 substitutions/site                                         
$ nw_labels constr.tree | xargs nw_prune -v example.constr.auto.treefile | nw_display - -w 60
                                      /--------------+ Human
                                      |                     
=-------------------------------------+ /-------+ Seal      
                                      | |                   
                                      \-+  /------+ Cow     
                                        \--+                
                                           \--------+ Whale 
                                                            
 |---------------|---------------|---------------|----      
 0             0.2             0.4             0.6          
 substitutions/site                                         
#
# The constraint+explicit model tree respects the constraint:
$ nw_labels constr.tree | xargs nw_prune -v example.constr.treefile | nw_display - -w 60
                                      /--------------+ Human
                                      |                     
=-------------------------------------+   /--------+ Seal   
                                      |  /+                 
                                      \--+\--------+ Whale  
                                         |                  
                                         \-------+ Cow      
                                                            
 |---------------|---------------|---------------|----      
 0             0.2             0.4             0.6          
 substitutions/site                                         
$ nw_display constr.tree -w 60
                           /-------------------------+ Human
 /-------------------------+                                
 |                         \-------------------------+ Cow  
=+                                                          
 |                         /-------------------------+ Seal 
 \-------------------------+                                
                           \-------------------------+ Whale

[AlesBucek]

I could not replicate the problem in following run (i.e. constraint was applied as expected):

module load iqtree/2.0.7
iqtree2 -s $InAln -nt AUTO -spp $InPart -m TESTMERGE -rclusterf 10 -g $ConstraintFile -bb 1000 -bnni -pre $OutDir

[alephreish]

@AlesBucek I cannot comment on your observation since you haven't provided a reproducible example. I've tested versions 2.0.3 and 2.1.2 which are available from conda with my minimal example above and they behave exactly as the latest version (2.3.0).

[iqtree]

Can you try adding -t PARS option to the command line and see if that solves the issue?

[alephreish]

@iqtree Nope, it doesn't solve the issue:

$ iqtree2 --version
IQ-TREE multicore version 2.3.0 COVID-edition for Linux 64-bit built Mar 14 2024
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
#
$ grep Command example.*.log
example.constr.auto.log:Command: iqtree2 -s /path/to/iqtree_env/example.phy -g constr.tree --prefix example.constr.auto -t PARS -redo
example.constr.TIM2.log:Command: iqtree2 -s /path/to/iqtree_env/example.phy -m TIM2+I+G -g constr.tree --prefix example.constr.TIM2 -t PARS -redo
example.unconstr.log:Command: iqtree2 -s /path/to/iqtree_env/example.phy --prefix example.unconstr -t PARS -redo
#
$ function plot_tree() { nw_labels constr.tree | xargs nw_prune -v "$1" | nw_reroot - Human | nw_order - | nw_topology - | nw_display - -w 20; }
# The constraint
$ plot_tree constr.tree
     /-------+ Cow  
     |              
 /---+   /---+ Seal 
 |   \---+          
=+       \---+ Whale
 |                  
 \-----------+ Human
                    
#                   
# Constrained tree with defined model
$ plot_tree example.constr.TIM2.treefile
     /-------+ Cow  
     |              
 /---+   /---+ Seal 
 |   \---+          
=+       \---+ Whale
 |                  
 \-----------+ Human
                    
#
# "Constrained" tree with ModelFinder
$ plot_tree example.constr.auto.treefile
         /---+ Cow  
     /---+          
 /---+   \---+ Whale
 |   |              
=+   \-------+ Seal 
 |                  
 \-----------+ Human
                    
#                    
# Unconstrained tree
$ plot_tree example.unconstr.treefile
         /---+ Cow  
     /---+          
 /---+   \---+ Whale
 |   |              
=+   \-------+ Seal 
 |                  
 \-----------+ Human
                                    

[thomaskf]

Hi @alephreish ,
Thanks for reporting the issue. This issue has been fixed. Please use the version 2.3.3 or later.
Thomas