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Replace BMGE with ClipKit #67
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enhancement
Highlight something that could be improved. Please be specific, TreeSAPP isn't perfect.
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cmorganl
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the
enhancement
Highlight something that could be improved. Please be specific, TreeSAPP isn't perfect.
label
Jan 8, 2021
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ClipKit parameters and settings have been benchmarked using for f in *_evaluate*/final_outputs/clade_exclusion_performance.tsv
do
echo $f
cat $f | awk '{sum+=$5*$7;} END {print sum;}'
done The parameter set with the lowest score will be used as the default. |
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Labels
enhancement
Highlight something that could be improved. Please be specific, TreeSAPP isn't perfect.
ClipKIT is a new MSA-trimming Python package. The authors indicate the trimmed MSAs generated by ClipKIT are more "desireable" (combined RF distance and bipartition supports) than those from competing tools, including BMGE.
Using ClipKit instead of BMGE would also clean up the installation process, by not having to package the BMGE.jar file with TreeSAPP. It could instead be installed using pip or conda.
treesapp/sub_binaries/
directory, and support for BMGE.jarThe text was updated successfully, but these errors were encountered: