Infer tree from multiple sequence alignment.


usage: gtdbtk infer --msa_file MSA_FILE --out_dir OUT_DIR
                    [--prot_model {JTT,WAG,LG}] [--no_support] [--gamma]
                    [--prefix PREFIX] [--cpus CPUS] [--tmpdir TMPDIR]
                    [--debug] [-h]

required named arguments


multiple sequence alignment in FASTA format


directory to output files

Named Arguments


Possible choices: JTT, WAG, LG

protein substitution model for tree inference

Default: “WAG”


do not compute local support values using the Shimodaira-Hasegawa test


rescale branch lengths to optimize the Gamma20 likelihood


prefix for all output files

Default: “gtdbtk”


number of CPUs to use

Default: 1


specify alternative directory for temporary files

Default: “/tmp”


create intermediate files for debugging purposes

## Files output



gtdbtk infer --msa_file msa.faa --out_dir infer_out


[2020-04-14 09:37:55] INFO: GTDB-Tk v1.1.0
[2020-04-14 09:37:55] INFO: gtdbtk infer --msa_file msa.faa --out_dir infer_out
[2020-04-14 09:37:55] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 09:37:55] INFO: Inferring FastTree (WAG, +gamma, support) using a maximum of 1 CPUs.
[2020-04-14 09:37:55] INFO: FastTree version: 2.1.10
[2020-04-14 09:37:55] INFO: FastTree version: 2.1.10
[2020-04-14 09:37:55] INFO: Done.