Writing out tables from TOPCAT is done using the Save Table Window. In general you have to specify the format in which you want the table to be output by selecting from the Save Window's Table Output Format selector; the following sections describe the possible choices. In some cases there are variants within each format - these are described as well.
The program has no "native" file format, but if you have no particular
preference about which format to save tables to,
FITS is a good choice.
Uncompressed FITS tables do not in most cases have to be read all the
way through (they are 'mapped' into memory), which makes them very
fast to load up.
The FITS format which is written by default
(also known as "FITS-plus") also uses a trick to
store extra metadata, such as table parameters and UCDs
in a way TOPCAT can read in again later (see Section 18.104.22.168).
These files are quite usable as normal FITS tables by other applications,
but they will only be able to see the limited metadata stored in the
For very large files, in some circumstances column-oriented FITS
colfits") format can be more efficient for some applications,
though this is unlikely to be understood except by STIL-based code
(TOPCAT and STILTS).
If you want to write to a format which retains all metadata in a portable
format, then one of the Section 22.214.171.124 formats might be better.