infer

Infer tree from multiple sequence alignment.

Arguments

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

--msa_file

multiple sequence alignment in FASTA format

--out_dir

directory to output files

Named Arguments

--prot_model

Possible choices: JTT, WAG, LG

protein substitution model for tree inference

Default: “WAG”

--no_support

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

--gamma

rescale branch lengths to optimize the Gamma20 likelihood

--prefix

prefix for all output files

Default: “gtdbtk”

--cpus

number of CPUs to use

Default: 1

--tmpdir

specify alternative directory for temporary files

Default: “/tmp”

--debug

create intermediate files for debugging purposes

## Files output

• [prefix].log

• [prefix].unrooted.tree

• [prefix].warnings.log

• infer/intermediate_results/

  • [prefix].fasttree.log

  • [prefix].tree.log

Example

Input

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

Output

[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.