The draw Wednesday of the top eight players - using numbered fortune cookies - put Federer in the Red Group along with Gilles Simon.
The second-ranked Federer became the top seed when No. 1 Rafael Nadal withdrew because of tendinitis in his right knee. Nadal pulled out of the Paris Masters last week.
Federer also dropped out in Paris, citing a sore back, but arrived ready to play in Shanghai.
Third-ranked Novak Djokovic is the top seed in the Blue Group, which includes Nikolay Davydenko; Jo-Wilfried Tsonga - who won in Paris to seal his spot in Shanghai - and Juan Martin Del Potro.
Simon, Tsonga and del Potro are playing in the Masters Cup for the first time. Simon was added to the field after the withdrawal of Nadal, who could be in doubt for Spain's Davis Cup final against Argentina on Nov. 21-23.
Murray, Tsonga and del Potro have dominated in the second half of the year. Murray had a 14-match winning streak ended in Paris by David Nalbandian, while del Potro rose from No. 50 at the start of the year to No. 8 by winning four titles and compiling a 32-match winning streak.
Tsonga, who lost the Australian Open final to Djokovic, has improved from No. 38 to No. 7.
The Masters Cup winner will take home $600,000. Next year, the event moves to London.
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