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README.md

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# Usage
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## Prepare input
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Now we're ready to run the workflow. First, create a folder that will contain the results.Here we call it `myfam`.
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Now we're ready to run the workflow. First, create a folder that will contain the results. Here we call it `myfam`.
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```
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mkdir myfam
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## Run Foldtree
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All we need to do now is run the workflow. In this example, we use 4 cores. We also have the option of filtering out structures with an average pLDDT < 40 (disabled by default). This was shown to improve the quality of trees relative to sequence-based trees (see the manuscript). Here we disable filtering to include all structures in the tree.
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All we need to do now is run the workflow. In this example, we use 4 cores. We also have the option of filtering out structures with an average pLDDT < 50 (disabled by default). This was shown to improve the quality of trees relative to sequence-based trees (see the manuscript). Here we disable filtering to include all structures in the tree.
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```
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foldtree --folder=myfam --no-filter -p

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