The Republic of Ireland international has been linked with a January move to Aston Villa, which would see him reunited with former Norwich boss Paul Lambert.
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"It was a combination of a few things," Hughton told reporters. "I chose on this occasion to go with two up front. There will always be questions on whether you should play one off the front or two up front.
"There's always the argument, whichever way you play it, that you should go the other way, but I thought it was quite brave of us to play two, to try stop [Everton] playing out from the back.
"Wes, of course, has played in the last couple of league games and was injured for the last game, so he very much came into my thoughts, but I decided to go with the two strikers up top.
"There is no situation, he is a Norwich City player. He was very much in my thoughts to play today and is very much a strong part of the squad."