Programs installed but not visible in application folder

I am having a strange problem.  Only a few of my programs are showing up in the application folder.  If I search for the programs using the finder window they are there and the path at the bottom of the finder window shows they are in applications,  and can be used but they just are not visible in the application folder (root folder).
Any suggestions how I can make these programs visible.
Thanks

Try this as a start:
Enable Finder to Show Invisible Files and Folders
Open the Terminal application in your Utilities folder.  At the prompt enter or paste the following command line then press RETURN.
defaults write com.apple.finder AppleShowAllFiles TRUE
killall Finder
To turn off the display of invisible files and folders enter or paste the following command line and press RETURN.
defaults write com.apple.finder AppleShowAllFiles FALSE
killall Finder
Alternatively you can use one of the numerous third-party utilities such as TinkerTool or ShowHideInvisibleFiles - VersionTracker or MacUpdate.
Do both items. Sometimes simply setting the Finder to show invisible files then turning off the option will make those invisible applications reappear. Sometimes it doesn't work. In that case you can try the following:
1. Enable the Finder to display invisible files. Leave the Terminal active.
2. Enter the following command line in the Terminal
sudo chflags -R nohidden
Put a space after "nohidden", select all the invisible applications you could not see and drag the selection into the Terminal window. Press RETURN. You will be prompted for your admin password. Enter it. It will not be echoed. Press RETURN.
3. Disable the Finder's display of invisible files.

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