Use this tool (uses the new apksigner from Google):
https://github.com/patrickfav/uber-apk-signer
Disclaimer: Im the developer :)
You need to generate a keystore once and use it to sign your unsigned apk.
Use the keytool provided by the JDK found in %JAVA_HOME%/bin/
keytool -genkey -v -keystore my.keystore -keyalg RSA -keysize 2048 -validity 10000 -alias app
zipalign which is a tool provided by the Android SDK found in e.g. %ANDROID_HOME%/sdk/build-tools/24.0.2/ is a mandatory optimization step if you want to upload the apk to the Play Store.
zipalign -p 4 my.apk my-aligned.apk
Note: when using the old jarsigner you need to zipalign AFTER signing. When using the new apksigner method you do it BEFORE signing (confusing, I know). Invoking zipalign before apksigner works fine because apksigner preserves APK alignment and compression (unlike jarsigner).
You can verify the alignment with
zipalign -c 4 my-aligned.apk
Use jarsigner which, like the keytool, comes with the JDK distribution found in %JAVA_HOME%/bin/ and use it like so:
jarsigner -verbose -sigalg SHA1withRSA -digestalg SHA1 -keystore my.keystore my-app.apk my_alias_name
and can be verified with
jarsigner -verify -verbose my_application.apk
Android 7.0 introduces APK Signature Scheme v2, a new app-signing scheme that offers faster app install times and more protection against unauthorized alterations to APK files (See here and here for more details). Therefore, Google implemented their own apk signer called apksigner (duh!)
The script file can be found in %ANDROID_HOME%/sdk/build-tools/24.0.3/ (the .jar is in the /lib subfolder). Use it like this
apksigner sign --ks my.keystore my-app.apk --ks-key-alias alias_name
and can be verified with
apksigner verify my-app.apk