On the command you can tell Taxnameconvert to exchange all names found in one specified column of name table file to the corresponding name in another specified column. The renaming takes place on the contents of a given sequence or tree file and either printed to screen or into a file with specified name.
The name table file is just a text file containing columns with different names for sequences like taxon name, 10-letter names (for PHYLIP files), common names, full names etc. The names can also contain spaces and can be bounded by quotes if desired during the renaming process. The latter is needed if the final names in treefiles contain spaces.
Taxnameconvert is a Perl-script, which means that Perl needs to be installed, but runs on all operating systems.
Further details can be found in the included README file or by typing taxnameconvert.pl -h. Sample files are included in the data folder.
NOTE: The program does not check whether a taxon name is prefix/postfix/infix of another, i.e., it is contained within another name. To prevent that parts of the longer names renamed, make sure that the longer name occurs first in the name table file.