I'm using the EMBOSS `transeq` tool to translate the first ORF of 26,000 sequences. Since the tool is pretty slow (takes ~1 minute per short sequence) and to make the process parallel, I split the fasta file into smaller files (down to one sequence per file) and then run `transeq` on each file. However, the sequences are renamed in the following format: `EMBOSS_001_1`.

How could I prevent `transeq` from renaming these sequences?

If nothing else works, I'll create a script that manages the translation of each individual sequences and makes sure to rename it after it has been translated.
Assuming that your input sequences are in [fasta sequence format][1] then one option which might help is to disable the parsing of the sequence identifier. By default [EMBOSS][2] attempts to identify the appropriate sequence format from the initial lines of the input. If the input is identified as being in a fasta sequence format variant (i.e. 'fasta' format) then identifier parsing will be used to extract information commonly encoded in structured identifiers, such as the database name, accession and entry name. For a list of possible fasta sequence format variants supported by EMBOSS see the ["EMBOSS Users Guide"][3] appendix ["A.1. Supported Sequence Formats"][4]. The additional processing can be disabled by specifying the generic 'pearson' format fro the input, which uses the first non-whitespace token on the header line as the sequence identifier. The input sequence format is specified using the `-sformat` option, so your command-line will look something like:

    transeq -frame 1 -sformat pearson -sequence inSeqFile.fa -outseq outSeqFile.fa

Please note that the EMBOSS 6.6.0 release contains a bug which makes the parsing of sequence identifiers consisting of two pipe separated fields (e.g. `db|seqId`) very slow, which might explain the poor performance you are seeing. A fix for this problem should be available in the post release patches (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/), and the issue did not appear in the previous release (EMBOSS 6.5.7).

 [1]: http://en.wikipedia.org/wiki/FASTA_format
 [2]: http://emboss.open-bio.org/
 [3]: http://emboss.open-bio.org/html/use/
 [4]: http://emboss.open-bio.org/html/use/apas01.html#SequenceFormatsFasta