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This repository has been archived by the owner on Feb 6, 2024. It is now read-only.
When I run IQ-TREE to produce a ML phylogeny using the command below, it creates it easily within an hour:
"./iqtree
-s CX.MSA.fasta
-alrt 1000
-m JTT+G+F
-nt AUTO"
When I add my constraint tree to this command, "-g constraint_CX.newick" the code quickly runs up to and stays stuck at the point below.
"Reading constraint tree constraint_CX.newick...
Creating fast initial parsimony tree by random order stepwise addition..."
I have run it up to four hours to see if it eventually moves forward, but to no avail. I have no warnings in my log, much less errors. What might be happening?
I have tried changing the file format (from .tre to .newick), ensured sequence names were formatted correctly, and made sure the tree had no root.
The text was updated successfully, but these errors were encountered:
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When I run IQ-TREE to produce a ML phylogeny using the command below, it creates it easily within an hour:
"./iqtree
-s CX.MSA.fasta
-alrt 1000
-m JTT+G+F
-nt AUTO"
When I add my constraint tree to this command, "-g constraint_CX.newick" the code quickly runs up to and stays stuck at the point below.
"Reading constraint tree constraint_CX.newick...
Creating fast initial parsimony tree by random order stepwise addition..."
I have run it up to four hours to see if it eventually moves forward, but to no avail. I have no warnings in my log, much less errors. What might be happening?
I have tried changing the file format (from .tre to .newick), ensured sequence names were formatted correctly, and made sure the tree had no root.
The text was updated successfully, but these errors were encountered: