Checkpointing to resume stopped run

Starting with version 1.4.0 IQ-TREE supports checkpointing: If an IQ-TREE run was interrupted for some reason, rerunning it with the same command line and input data will automatically resume the analysis from the last stopped point. The previous log file will then be appended. If a run successfully finished, IQ-TREE will deny to rerun and issue an error message. A few options that control checkpointing behavior:

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http://www.iqtree.org/doc/Command-Reference

Check this link:http://www.iqtree.org/doc/Command-Reference

Hi Adriana & Jack,

Thank you for your prompt response in this question. According to the command-reference, it is easy to define an outgroup in IQ-TREE. However, but I don't find any option to specify several outgroups.

Hi,

I am struggling with the same issue. I would like to define multiple sequences as an outgroup which are in paraphyletic genus, but I can't find a way to do that. Can anybody help?

It really seems unlikely that IQtree can define just one sequence as an outgroup....

Thanks,

Maja

Hi all. In most phylogenetic tree inference programs the tree rearrangements and likelihood calculations are done with unrooted trees (unless you are dealing with time-calibration, which is usually, but not always, done after a tree has been reconstructed). So in most cases, the outgroup is used after a tree has been inferred, to reorient the topology before saving the file (IQTree and RAxML do this). This means that you can run an analysis without an outgroup, and reroot the tree manually at the desired position (between the monophyletic ingroup and outgroup taxa) in a program such as Figtree, Dendroscope, the package APE for R, Mesquite, Seaview, and so on.

Hi Teo,

thanks :) I figured you can, and I always do that after the analysis (for me FigTree is the best), but some people say you need to define it prior the analysis....not sure why. Can it affect the analysis itself?

It's late here to answer. But since v1.6.2, IQ-TREE supports a comma-separated list of outgroup taxa for -o option.

Bui Quang Minh Many thanks for your answer!

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