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** Using command line, you have to compile your program using: <code>javac -cp <JARs> <YourClass>.java</code> where <code><JARs></c * Run your program:

...tion that can be installed in a local Galaxy server, and as a command line program. The command-line program behind the web-application is a Jar as well, so Java is required on the ser

Here, we provide a command line program that uses an interpolation for precision-recall curves (and ROC curves) tha

== Program ==

...tion that can be installed in a local Galaxy server, and as a command line program. The command-line program behind the web-application is a Jar as well, so Java is required on the ser

...tion that can be installed in a local Galaxy server, and as a command line program. The command-line program behind the web-application is a Jar as well, so Java is required on the ser

...tion that can be installed in a local Galaxy server, and as a command line program. ...also provide a command line program and a web-application of a prediction program that can be used to predict binding sites for motifs discovered by Dimont i

* [[GeMoMa]]: Gene Model Mapper (GeMoMa) is a homology-based gene prediction program that uses the annotation of protein-coding genes in a reference genome to i

...expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor (see documentation below), which can be used to pred In addition to the Dispom binary, we also provide a program (DispomPredictor.jar) that can be used to predict binding sites using an al

...]. In the following we describe our approach and provide a download of the program used to make the predictions for the challenge and its source code.

Here, we provide a suite of tools including the EpiTALE program itself but also auxiliary tools for converting methylation data and chromat * [http://www.jstacs.de/downloads/EpiTALE-0.1-win.zip Windows program]: ZIP archive containing the EpiTALE Jar, all required Java modules, and a

...''ne '''Mo'''del '''Ma'''pper (GeMoMa) is a homology-based gene prediction program. GeMoMa uses the annotation of protein-coding genes in a reference genome t ...per transcript prediction. For unlimited use, please use the command line program or integrate GeMoMa in your own [https://galaxyproject.org/ Galaxy] instanc

...l SafeOutputStream] is a simple way to switch between writing outputs of a program to standard out, to a file, or to completely suppress output. This class is

...der.html SubclassFinder], or its parameters shall be set in a command line program using the [http://www.jstacs.de/api-2.0//de/jstacs/parameters/ParameterSetT

* Exceptions in multi-threaded code now lead to exit of program instead of only stopping the thread

...www.jstacs.de/downloads/AnnoTALEcli-1.5.jar runnable Jar]. For running the program and a quick help, type

<td>repair (if a transcript annotation can not be parsed, the program will try to infer the phase of the CDS parts to repair the annotation, defa <td>repair (if a transcript annotation can not be parsed, the program will try to infer the phase of the CDS parts to repair the annotation, defa