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Nearly two-thirds of all sequences were assigned with a genotype tag, and these were designated as set A. The remainder were temporarily designated as set B. GroupScan Analysis (described below) using the known set A for each sequence in Set A and B was carried out by batch command.
The power analysis was conducted using a batch command program in the HYPHY v0.99 package.
Measures of branch support [ 21, 23, 61, 62] were accomplished using batch command files in PAUP*, and the resulting log files were imported into an Excel spreadsheet for final calculations.
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The NIST MS PepSearch program is a batch command-line version of the NIST MS search GUI program.
Special operation commands: The McRAIT controller can invoke special operation commands such as batch commands.
Learn basic Batch commands.
Learn some basic batch commands.
Be sure you know what you are doing, and that none of the code is dangerous (e.g. batch commands to delete files).
Driving a rover involves little more than uploading a batch of command macros (control M is a right turn) to Mars each morning.
All the editing was performed using 'Batch conversion' command of software.
PAUP* also has the benefit of a more intuitive interface with the option of batch file command input, so here we focus only on the methodology using PAUP*.
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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