MSA tool for marker gene alignment

[Andrzej_Zielezinski]

Hi GTDB Team,

Thank you for the incredible resource that GTDB provides! I was wondering, which MSA tool is used to align marker genes in your pipeline?

Thanks in advance,
Andrzej

[donovan.parks]

Hi Andrzej,

Marker genes are aligned against the Pfam or TIGRfam HMMs listed in:

• https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/bac120_msa_marker_info.tsv
• https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/ar53_msa_marker_info.tsv

Alignment is done with the HMMER package: GTDB - Methods

Cheers,
Donovan

[Andrzej_Zielezinski]

Hi Donovan,

Thanks for clarifying, and apologies for overlooking that in the Methods section.

Best wishes,
Andrzej