Dear all,
I am using MALT 0.4.1 and I would like to know the difference between -id and -mpi parameters. In the manual, both are indicated as minimum percent identity; however, -id is under Filters and -mpi in LCA parameters.
Could somebody clear this, please?.
Many thanks!
Cheers
The -id option refers to filtering: only alignments that have or exceed the specified percent identity are reported the by the aligner
The -mpi option refers to the LCA algorithm: when placing a read taxonomically, only alignments that that have or exceed the specified percent identity are used in the LCA calculation.
In particular, it wouldn’t make sense to set -mpi lower than -id…
Thank you Daniel for the clarification!
Cheers