In Alfresco both the keystore and truststore file types are Java Keystores stored in one of the formats JKS, JCEKS, or PKCS12. We use a keystore and a truststore when Alfresco needs to communicate over SSL/TLS.
Usually, these are password-protected files that sit on the same file system as a running Alfresco instance. The default format used for these files is JKS until Java 8.
Since Java 9, though, the default keystore format is PKCS12. The biggest difference between JKS and PKCS12 is that JKS is a format specific to Java, while PKCS12 is a standardized and language-neutral way of storing encrypted private keys and certificates.