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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
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Cannot find ALISIM model information as outlined in concordance tutorial #156

Open aldendirks opened 7 months ago

aldendirks commented 7 months ago

There is no ALISIM information in concat.log as the tutorial states (visible to my eyes with a manual checkover and also confirmed with cat concat.log | grep "ALISIM". I do see information on ALISIM in the concat.iqtree file visible with tail -n 100 concat.iqtree. This is the relevant section: 

ALISIM COMMAND
--------------
To simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis, you can use the following command:

--alisim simulated_MSA -t concat.treefile -p /nfs/turbo/lsa-tyjames/mycology/Alden/analysis/busco_phylogenomics/2024-01-06_iqtree2/trimmed_alignments.best_model.nex

Is this the information I can use in the likelihood sCF command? Do I specify -m trimmed_alignments.best_model.nex?

By the way, this file actually doesn't exist for me... maybe it is referring to concat.best_model.nex. The directory with the alignments is called trimmed alignments but prefix was set to "concat".

Thanks for your help!

bqminh commented 3 months ago

If it's not too late, what was the command you used to run iqtree in the first place?

trongnhanuit commented 2 months ago

Hi @aldendirks, Thank you for using IQ-TREE/AliSim. Your bug report contains 3 questions, please find my answers below.

There is no ALISIM information in concat.log as the tutorial states (visible to my eyes with a manual checkover and also confirmed with cat concat.log | grep "ALISIM". I do see information on ALISIM in the concat.iqtree file visible with tail -n 100 concat.iqtree.

=> To improve the visibility, we changed to output AliSim command to the main output of IQ-TREE (i.e., .iqtree file) instead of the log file (i.e., .log, which captures everything from the console). I updated the relevant tutorial (on IQ-TREE wiki), which will be synchronized to IQ-TREE doc later.

Is this the information I can use in the likelihood sCF command? Do I specify -m trimmed_alignments.best_model.nex?

=> I need to discuss this with @bqminh @roblanf. Will come back to you once I've got the answer.

By the way, this file actually doesn't exist for me... maybe it is referring to concat.best_model.nex. The directory with the alignments is called trimmed alignments but prefix was set to "concat".

=> Yes, it should be concat.best_model.nex. This is a bug, which has been fixed. This bug fixed will be included in the next release of IQ-TREE.