By default pangolin will run the pangoLEARN model to assign the most likely lineage out of all currently designated lineages) and scorpio to assign specific lineages of interest by presence of constellations.
Pangolin 3.0 can optionally run a fast parsimony-based lineage assignment using UShER as the inference engine.
In the process of lineage assignment, pangolin creates an alignment using minimap2 to map against an early, anonymised reference SARS-CoV-2 sequence and then using gofasta to generate a fasta file from that mapping with the non-coding regions masked out with N's. For convenience (I know I certainly find it very useful for quickly generating a SARS-CoV-2 alignment), pangolin has a flag that will output this alignment in addition to the lineage report instead of writing it to temp. The exact parameters can be found in the source code here.
pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages positional arguments: query Query fasta file of sequences to analyse. optional arguments: -h, --help show this help message and exit -o OUTDIR, --outdir OUTDIR Output directory. Default: current working directory --outfile OUTFILE Optional output file name. Default: lineage_report.csv --alignment Optional alignment output. -d DATADIR, --datadir DATADIR Data directory minimally containing a fasta alignment and guide tree --tempdir TEMPDIR Specify where you want the temp stuff to go. Default: $TMPDIR --no-temp Output all intermediate files, for dev purposes. --decompress-model Permanently decompress the model file to save time running pangolin. --usher Use UShER model instead of default pangoLEARN --usher-tree USHER_PROTOBUF UShER Mutation Annotated Tree protobuf file to use instead of --usher default from pangoLEARN repository or --datadir --max-ambig MAXAMBIG Maximum proportion of Ns allowed for pangolin to attempt assignment. Default: 0.3 --min-length MINLEN Minimum query length allowed for pangolin to attempt assignment. Default: 25000 --verbose Print lots of stuff to screen -t THREADS, --threads THREADS Number of threads -v, --version show pangolin's version number and exit -pv, --pangoLEARN-version show pangoLEARN's version number and exit -dv, --pango-designation-version show pango-designation version number and exit --update Automatically updates to latest release of pangolin and pangoLEARN, then exits