Auxiliary Matters

Once again, a little rant: most native English speakers don't know what an auxiliary verb is. But let that not stop us from learning...

To Have or Not to Have

When "have" is an auxiliary, the negative form is "have not" and the interrogative form is "have ...?" On the contrary, when "have" is the main verb, with its full meaning of "to possess," or in the phrase "have to...," the negative form is "does not have" and the interrogative form is "does... have... ?". Examples:

WrongRight
They have not the same number of linesThey do not have the same number of lines
Has it to be initialized?Does it have to be initialized?
They do not have been initializedThey have not been initialized [the real verb is "to be," "have" is the auxiliary that combines with the verb to form the present perfect, "have been"]
Does the program have closed the file?Has the program closed the file? [the verb in this sentence is "to close"]

Do's and Don't's

The difference between auxiliaries and main verbs is made even more striking when considering the verb "to do." In a sentence like "They did not do much to solve the problem," "did" is an auxiliary, but "do" is the main verb, with its full meaning of "perform." As the example shows, the negative form of the auxiliary "did" is simply "did not," but the negative form of the verb "do" is "does not do" (or, in the example, "did not do" is the negative form of "did").

To Be or Not to Be

In some languages, in particular French, the auxiliary used to form the present perfect and other composite tenses is not always "have." Sometimes "be" can be used, for instance with intransitive verbs. In English, only "have" is used to form past composite tenses, "be" is only used to form the passive voice. Hence:

WrongRight
This signal is appearedThis signal has appeared

Using the Auxiliary for Emphasis

If you write "we did modify this program," it almost means that someone is accusing you of not having done so. If there is no reason to be defensive, simply say: "we modified this program."