Can blat use more than one core/CPU to speed up the alignment? I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU. However, is this programme able to use more than one core / CPU to speed up the alignment?

I cannot find such option in the help page of the tool here.

I installed blat using conda install -c bioconda blat.

I am using the latest version of blat, i.e. 36.
BLAT can only use one CPU. It is actually not the right tool for full-genome alignment. For "two versions" of the same species, MUMmer and minimap2 are orders of magnitude faster and probably give better alignment.

EDIT (moving comment to answer): OP comments that the purpose of this alignment is for lifting over annotations using the UCSC PSL-based pipeline. So far there are no converters for minimap2's SAM/PAF or MUMmer's delta formats. With the UCSC pipeline, you have to write a converter by yourself. An alternative approach is to use minimap2's liftover. The minimap2 cookbook gives an example:

minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa &gt; ecoli_canu.paf
echo -e 'tig00000001\t200000\t300000' | paftools.js liftover ecoli_canu.paf -


Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.