The Sequence Name Annotation-based Designer (SNAD) at:

http://veb.lumc.nl/SNAD/index.cgi

is very good for this. It can take an alignment, a tree (Newick format for example), or a list of names, and convert the names based on GenBank or UniProt database annotation.

I am attaching an output for your data, where I asked for genus and species information for each sequence, but given that they are all from H pylori, this was not a good choice.

The LANL HIV Databases has a tool for taking an alignment plus a spreadsheet of data to rename the sequences in the alignment:

https://www.hiv.lanl.gov/content/sequence/ALIGN_MULTITOOL/align_mt.html

use the RENAME tab at the top of this tool.

cat VacAFASTA1000.fasta | cut -d " " -f1 > shortname_VacAFASTA1000.fasta

This will trim the fasta header after the first space in fasta header

>tr|A0A1Y3E563|A0A1Y3E563_HELPX Toxin OS=Helicobacter pylori SS1 OX=102617 GN=X568_02390 PE=4 SV=1

TO

>tr|A0A1Y3E563|A0A1Y3E563_HELPX

Or use delimiter you want instead of space

The Sequence Name Annotation-based Designer (SNAD) at:

http://veb.lumc.nl/SNAD/index.cgi

is very good for this. It can take an alignment, a tree (Newick format for example), or a list of names, and convert the names based on GenBank or UniProt database annotation.

I am attaching an output for your data, where I asked for genus and species information for each sequence, but given that they are all from H pylori, this was not a good choice.

The LANL HIV Databases has a tool for taking an alignment plus a spreadsheet of data to rename the sequences in the alignment:

https://www.hiv.lanl.gov/content/sequence/ALIGN_MULTITOOL/align_mt.html

use the RENAME tab at the top of this tool.

Both previous answers are helpful. If you in the end don’t care much about the sequence names anymore, you can also simply replace them by short string and a number or similar (https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/simplifyFastaHeaders.pl). I do this if some software may be unhappy with the | character that will still be there using the first answer, or if I need even shorter headers.