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First, reads from different genotypes were mapped to aflatoxin gene cluster from A. flavus AF13 using Bowtie v1.1.1 (Langmead et al. 2009) and the resulting BAM file was fed to SAMTools v0.1.16 (Li et al. 2009).
For SSR and SNP detection, EST sequences were clustered with CAP3 using default parameters and the resulting ".ace" format assembly file was fed into the corresponding programs.
A Cdx-FMN-CPR sequence alignment file was fed into Sculptor implemented in the Phenix package along with the Protein Data Bank (PDB) file of the CPR-FMN domain without the FMN cofactor (PDB entry 1B1C).
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After model creation the XSM file is fed to the simulator.
It follows a similar workflow as 3D printing: A digital file is fed into the machine, and then the mill does the rest of the work.
The image files are fed to the model that outputs a binary vector to indicate whether the terms are annotated.
After obtaining the pre-processed file, it was fed as input to construct the graph object (either undirected or directed).
Dreamcatcher was fed files of a normal swingarm that had been produced by earlier versions of CAD software.
Arachne was fed files from NCBI, slightly modified to satisfy the input parser.
Paintomics was fed with data files and run with default parameters, selecting A.thaliana at the species check-box.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com