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Liu and Ning generated an implementation library and an executable package for ECC.
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The source code and executable package of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf.ku.edu/EDTSurf
Sequences were compared with the GenBank non-redundant (nr) protein database using the standalone Blastx program found in an executable package as previously described [ 40].
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The application was entirely written in Java and distributed as an executable jar package.
This was performed through the codeml executable of the PAML4 package [ 54].
The core of the CHP process details the tools and command lines for the different steps of the analysis, which in this case consists mainly of different executables of the deepTools package (12), MACS2 (13) for peak calling and two custom scripts.
In addition, it might be convenient to also add the HiCUP_digester step of the pipeline to the main HiCUP executable The link to the software package was identical to the version control system link, and it was not straightforward to find the link to the self-hosted bug report system.
The software package contains the executable and a set of Perl scripts for PPI extraction.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com