The decoded audio can be the same
FLAC and Apple Lossless Audio Codec reduce file size without discarding the represented PCM data. If a FLAC and an ALAC file were made from the same source with no other processing, decoding either can produce the same samples. One codec is not inherently more detailed or higher resolution.
FLAC has a direct file identity
FLAC commonly uses the .flac extension, making the
codec obvious from the filename. It is widely supported by music
servers, network receivers, tagging tools, and players outside the
Apple ecosystem. FLAC can also appear inside an Ogg container, so
probing still matters.
ALAC commonly lives in MPEG-4 Audio
ALAC is usually stored in an .m4a container. That same
extension can hold lossy AAC or PCM, so an M4A filename does not
establish that a file is lossless. Nyquist inspects the payload
where possible and reports the codec it finds.
File size is not a quality score
Compression settings and the structure of the audio can make one lossless file smaller than another. As long as both files are valid lossless encodes of the same source, a size difference does not mean the smaller one discarded samples.
Which should you keep?
Choose based on the devices and tools around the library. FLAC is often the more portable choice across mixed platforms and network hardware. ALAC integrates naturally with software that expects MPEG-4 Audio. Nyquist supports both for local playback, metadata display, and analysis; compatible UPnP/DLNA receivers can receive the original file.
See the complete audio-format reference or read what lossless audio does and does not prove.