How can I include alertify.js in an .php file?

Good.

The way you use to login does not work well with the alertify.js library. Alertify js works well with asynchronous requests (ajax in jquery).

I recommend that you use asynchronous requests, for which you must deactivate the action of the form and put a code like the following in JS (this is an example, but there is enough code in this question ):

$(document).ready(function () {
    $('input#botonEnviar').click( function() {
        $.post( 'url_login', $('form#myForm').serialize(), function(data) {
               alertify.alert(data);
           },
           'json'
        );
    });
});

Also add resources to alertify (change according to your case):

<!-- include the script -->
<script src="{PATH}/alertify.min.js"></script>
<!-- include the style -->
<link rel="stylesheet" href="{PATH}/alertify.min.css" />
<!-- include a theme -->
<link rel="stylesheet" href="{PATH}/themes/default.min.css" />

And return a message from the server in json format or in text flat, depending on the configuration you have in the asynchronous request.

The other option is to save the messages in the session and redirect to the view correct with header('Location: '.$newURL); from php. not with window.location.href of javascript. An example is more or less like this (these types of messages are usually found on the internet as " Flash messages ", although they are generally used within a framework, they are saved in the session and only last until the next http request:

if (mysql_num_rows($resultado) > 0) {
        session_start();
        $_SESSION['usuSession'] = $cor;
        header('Location: ../html/Index.php');
        exit;
    } else {
        $_SESSION['msg'] = 'El login ha fallado';
        header('Location: ../html/Login.html');
        exit;
}

then in your Login.php view you put a code like the following:

<form>
    <!-- mensaje de login -->
    <?php if(isset($_SESSION['msg'])) {
             echo $_SESSION['msg'];
             unset($_SESSION['msg']);
          } ?>
    <input>usuario</input>
    <input>contraseña</input>
</form>

Good. This is the idea, to make it work you have to elaborate it more. It's night and for time I can not write something more decent :(

(I hope someone edits this so that it works: P)

I do not know if I understood your question well but you can put before opening php

<script src="tucarpeta/alertify.min.js"></script>

or after closing? >

<script src="tucarpeta/alertify.min.js"></script>