A verb phrase consists of a main verb and its auxiliaries. In this sentence, will have been studying is a combination of auxiliary verbs (will have been) and the main verb (studying), forming a future perfect continuous tense.
"By the time he arrives, we will have finished the project."
"Will have" is the correct future perfect tense structure,
Indicating that the action of finishing the project will be completed before a specified future time (when he arrives).
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