trim_msa¶

The trim_msa command will trim a MSA given a user-specified mask file, or the archaeal/bacterial mask present in the reference data.

Arguments¶

Example¶

Input¶

gtdbtk trim_msa --untrimmed_msa msa.faa --output msa_trim.faa --mask_file mask.txt

#### msa.faa

>genome_a
AKLAK

#### mask.txt

Output¶

[2020-04-13 10:25:13] INFO: GTDB-Tk v1.1.0
[2020-04-13 10:25:13] INFO: gtdbtk trim_msa --untrimmed_msa msa.faa --output msa_trim.faa --mask_file mask.txt
[2020-04-13 10:25:13] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-13 10:25:13] INFO: Done.

#### msa_trim.faa

>genome_a
KAK