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).

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