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Sample files for individual codes are provided on the help pages (look for the white I in a blue dot). Here are some issues we are aware of with specific codes. If you have an issue with a specific code, we encourage you to visit the code's specific User group.
IQ-Tree. User group is here
Geneious Plugin: On Windows machines with High-Res screens (e.g. 3840 x 2400), default display settings may cause some windows to extend beyond the available viewing area. You can access all optons by resetting the value Settings/System/Display/Scale from the default 300% to a value less than or equal to 250%. Also, if you "Reset to Defaults" using the dropdown on the lower left side of the page, ALL of the IQ-Tree pages will reset to default, not just the page you are on.
BEAST/BEAST2: User Group is here:
Run Failures: Some jobs fail to run because of an incompatibility with BEAGLE. The error is in BEAST, and the developers are working on these issues. In the meantime you can run (slowly) using BEAST without BEAGLE, just check the box in the parameter page that says: Do not use Beagle.
MrBayes: Issues are reported here:
MrBayes Blocks: The interface for MrBayes will overwrite values in the MrBayes block UNLESS the interface is deactivated by checking the box that says "My Nexus file has a MrBayes block." There is no planned fix for this issue, user caution is required.
Setting nruns and nchains: Making at least two runs is always recommended.The reason for doing two "runs" is to see whether they obtain similar consensus trees and parameters. The interface permits nruns=2 and nruns=4. Running odd numbers is inefficient AND slows your run down. The MrBayes manual says: "By default, Nchains is set to 4, meaning that MrBayes will use 3 heated chains and one "cold" chain. In our experience, heating is essential for problems with more than about 50 taxa, whereas smaller problems often can be analyzed successfully without heating. Adding more than three heated chains may be helpful in analyzing large and difficult data sets."
Based on this information, we recommend that users set Nruns=2 and Nchains=4, but the interface limits nruns*nchains to be <= 16 and nruns*nchains must be a multiple of 2.
If there is a tool or a feature you need, please let us know.
RAXML/RAXML-NG: User Group is here. The creators of RAxML prefer users switch to RAXML-NG, which is currently under active development.
Multiple Outgroups: When specifying more than one outgroup, do not introduce blank spaces. Use outgroup1,outgroup2 not outgroup1, outgroup2. In the latter case you will see the following error message “Error, you must specify a model of substitution with the ‘-m’ option”
GARLI: Garli User Forum (not currently active) is here:
For unknown characters the default is "?", although with Nexus you can define it to be whatever you want. Thus, a Nexus dataset that uses only X and not ? could be read fine by adding missing=X to the Format line. If the dataset is in non-Nexus format (usually Phylip), then the only options are ? and -. In all cases the gap character, by default "-", is treated identically to a missing character.
If there is a tool or a feature you need, please let us know.
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