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1. Obtaining CView

1.1 A zip (cview.zip) file containing the CView.jar, license agreement and quick start guide can be downloaded from the Files tab of the sourceforge url: https://sourceforge.net/projects/cview/.

1.2 CView has been tested on Ubuntu 20.04, Windows 10 and MacOS High Sierra, but it is usable on any operating system with installed Java Runtime Environment (JRE) 8.0 or higher. To find out what version of Java is running open a terminal window and type java -version. If an update is required the latest JRE's can be obtained from the Oracle website: https://www.oracle.com/java/technologies/javase-downloads.html

1.3 Extract the contents of the .zip file and place the CView.jar file within the desired directory. Make sure permissions are set on this file so that it can be executed. To do this right click and use the properties tab OR chmod the file (sudo chmod +x).

2. Running CView

2.1 As long as the CView.jar file has been given permission to be executed (1.3), CView can be launched by double clicking on the file. Alternatively, a terminal window can be opened and the user can use the command: java -jar path-to-CView.jar.

2.2 Input data must be a multiple sequence alignment in fasta format. CView is an alignment viewer and will not work on unaligned sequences.

3. Sample Data

Within the cview.zip file is also a file called “test_data_HIV_1_GP120_CCR5_US.fasta”. This is an alignment in FASTA format containing HIV-1 sequences from North America that have been identified as CCR5-using, the later being a co-receptor that the virus can use. More details on this dataset are in the use-case scenario of the publication that describes CView. This alignment can be loaded using the “All Sequences” -> “Load Fasta” menu uption.

4. Obtaining Source Code

Alternatively the code can be downloaded from the Code tab, imported into an IDE, such as Netbeans, and recompiled as desired. The steps below are for the Netbeans IDE, but others will have a similar process. Note: this is not the recommended (nor required) path for obtaining the working software, unless there is a specific requirement to edit the code. Steps to do this are:

4.1 On the code tab of the project obtain the read only svn checkout link (svn://svn.code.sf.net/p/cview/code/). There are three options: (i) SSH, (ii) HTTPS and (iii) RO. The read only option is RO and does not require a password later.

4.2 Open Netbeans and under the Team menu select the sub menu Subversion and then sub-sub menu Checkout. This will open a small window with some field to fill.

4.3 In the field that is labelled Repository URL place the RO svn checkout link obtained in step 1.4.1. The username and password can be left blank. Click next.

4.4 Use the browse button to browse the project Repository Folders and select the core folder. This contains all the code. Once OK is pressed select the local folder where you want to download the code to e.g. testFolder.

4.5 Click finish. All the code files and subfolders within core folder will then be placed into the selected location.

4.6 These can be used to set up a new project within Netbeans and you can begin to edit and recompile the code. The easiest way to do this is to creating a new project from scratch and then past the core folder into the source directory of the new project.