what are the differences between PHP base64_encode and *nix base64

open console in your browser, type atob('dGVzdAo='):

_{(source: gyazo.com)}

You have extra character in your input. And that is 0x0A (LF).

The linux base64 has a new line at the end.

When doing an echo it gives me this:

MacPro:~ bardiir$ echo 'test'
test
MacPro:~ bardiir$ 

I'd guess you might have an included line-ending in the unix one as echo is probably appending a newline character even if you pipe it throuch to the base64 encode.

echo usually outputs a new line character at the end of the string, to suppress that use the -n switch:

$ echo -n 'test' | base64
dGVzdA==

Similarly for PHP:

$ php
<?php
echo base64_encode("test\n");
?>
dGVzdAo=