As the CIA and U.S. Special Forces battle to eliminate the leadership of al-Qaida in Yemen, strains are building with embattled President Ali Abdullah Saleh who wants the Americans to focus on crushing rebels seeking to topple him.

Saleh has been in power in 1978 and his longevity is due in considerable part to his frequent alliances with Yemen's Islamists. Indeed, he defeated a southern secessionist movement in a 1994 civil war largely because of the support of large numbers of Islamist fighters.

Many were Arab veterans of the 1979-89 war in Afghanistan against Soviet forces who formed the core of al-Qaida when it was formed in 1998 by Osama bin Laden, whose family hails from Yemen.

Saleh doesn't see the al-Qaida in the Arabian Peninsula, which operates out of Yemen, as a major threat; at least not as dangerous as his political opponents, including high-level defectors from the military, who are battling to bring about his downfall.

What began as a popular pro-democracy uprising against his authoritarian and corrupt regime in January has become more of a civil war.

Amid the anarchy, AQAP and its jihadist ally, the Army of Abyan, has taken over several cities and towns in the southern provinces of Abyan and Shabwa since May.

At the same time, the CIA and the U.S. military's Joint Special Operations Command have sharply escalated covert operations against AQAP, particularly its leadership.

Washington considers AQAP more dangerous to the United States than any other al-Qaida grouping following a series of attacks over the last two years.

On Sept. 30, a CIA unmanned aerial vehicle, flown from a secret base on the Arabian Peninsula, assassinated Anwar al-Awlaki, AQAP's senior ideologue and recruiter, with Hellfire missiles in Yemen's al-Jawf province east of the capital Sanaa.

Awlaki, born in New Mexico to Yemeni parents, was the first U.S. citizen to be placed on the CIA's kill-or-capture list. U.S. President Barack Obama sanctioned the assassination.

U.S. officials described Awlaki as AQAP's external operations chief but U.S. and European counter-terrorism experts have said the Americans branded him as such to justify the order to assassinate him.

The Americans insist that AQAP seeks to join forces with al-Shabaab, a jihadist group operating in Somalia across the Gulf of Aden to mount attacks against the United States.

That premise too has been questioned by counter-terrorism specialists, primarily because al-Shabaab is dominated by clan leaders with a more nationalist agenda, overthrowing the Western-backed regime installed in Mogadishu in December 2006.

But al-Shabaab includes several dozen Somali-Americans who're seen as ideal recruits to carry out attacks on the United States because they can blend into the social fabric.

It could be it is these men AQAP wants to gets its hands on.

All this puts the Americans in an awkward situation: they depend on Saleh's counter-terrorism units -- largely U.S.-trained -- for intelligence on AQAP while at the same time seeking to pressure Saleh to step down.

At the same time, Saleh complains that the U.S. airstrikes, by drones or combat jets, intensifies the opposition to his regime because the Americans are seen as his allies.

"Even as the United States delivers blows against AQAP, it risks being drawn into the government's brutal southern counterinsurgency in a manner that could strengthen the group," says counter-terrorism specialist Michael Knights of the Washington Institute for Near East Policy.

"Indeed, Yemen is a place where the United States is seen by many locals as being on the wrong side of the Arab Spring, while Al-Qaida affiliates appear by some locals to be standing 'with the people'."

The south, as mentioned above, has long sought to secede from the north, where Saleh's regime is based. The two parts of Yemen were separate until they united in 1990.

Only four years later, they went to war when the south, formerly the socialist People's Democratic Republic of Yemen, sought to break away from the tribal, deeply Islamic north.

The current conflict has acquired an Alice in Wonderland patina, with U.S. operations, and the attendant civilian casualties, driving Yemenis into AQAP's embrace.

Meanwhile, says Knights, "The Saleh government seeks to perpetuate the war in the south because the fighting will force Washington to choose between reform and counter-terrorism, with the latter likely to win out."