*.hmmtblout.besthit.sim.fa

These files can be found under the mt_assembly directory if you use the mitoz all command. If you use the mitoz findmitoscaf command, you can also find these in your working directories.

They are the initial candidate mitochondrial sequences, directly from the HMMER program.

One of the very important usages is that you can compare the *.hmmtblout.besthit.sim.fa files from different samples via the Blast program, and check for highly similar sequences. By doing so, you can identify potential cross-contamination among your samples. You can even blast these files again a local NT database or NCBI online NT database, and get an idea of taxonomic assignment results.