You can run zipalign manually in command line:
zipalign [-f] [-v] <alignment> infile.apk outfile.apk
Note that zipalign is located inside ${sdk.dir}\tools
For more details visit zipalign
[Update]
Also, If you need to sign it you can run:
jarsigner -verbose -sigalg SHA1withRSA -digestalg SHA1 -keystore YOURKEYSTORE unsigned.apk alias_name
(jarsigner is located inside java JDK_HOME/bin)