Cavendish and Alaphilippe have both been left out of the eight-man Quickstep-AlphaVinyl team to be taken to the Tour de France, following the official team announcement on Monday (AEST).
Cavendish had won the British national road race championships on Sunday and claimed the green jersey in France last year, but Quickstep-AlphaVinyl have opted for Dutchman Fabio Jakobsen as the lone sprinter to be selected for the team, with his impressive form resulting in ten stage victories this year.
"Overall, the race has something for everyone, and that’s why we are going there with a balanced team”, said Quickstep AlphaVinyl sports director Tom Steels.
"Fabio has proved how fast and strong he is in the sprints and will now get to discover Le Tour."
Cavendish has instead been named as a reserve for the race alongside new French national champion Florian Sénéchal, with Tour debutants Jakobsen, Mikkel Honoré and Andrea Bagioli being named in their place.
“Concerning our reserves, we must stress out that they showed a lot of professionalism, continued to train and remained focused in these past couple of weeks, and even brought two victories at the Nationals," Steels added.
Alaphilippe has been left out of the squad altogether, as the 30-year-old has struggled to recover from the injuries sustained from a crash at Liège–Bastogne–Liège two months ago.
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After suffering a punctured lung, fractured ribs and a fractured shoulder blade, the Frenchman has since tried to regain his form in time for the three-work Grand Tour but suffered another injury setback when he complained of a stomach problem at the recent national championships.
"The decision to leave Julian home was a very difficult one, as he is one of the team’s most emblematic riders and we wrote so many great moments together at the Tour," Steels said.
"Julian worked hard to get back into shape after what happened to him in Liège, but it is felt that for a rider like him it’s always important to be on top of his game and be able to compete with the best riders of the peloton in a race like Le Tour."
"I'm disappointed to not be at the Tour de France this year," Alaphilippe said.
"To miss another opportunity to wear my beautiful rainbow jersey in my home country is very sad for me and I knew that this decision would be difficult for the team to take. At the same time, I completely understand this, because I too don’t want to be at the start if I can’t be at my best level."
Kasper Asgreen, Mattia Cattaneo, Tim Declercq, Yves Lampaert and Michael Mørkøv will round out the the Quickstep-AlphaVinyl team to be taken to France for the race which will also see 2020 green jersey winner Sam Bennett absent, with the Bora-Hansgrohe rider still recovering from COVID-19.