hierarchical multiple sequence alignments (hiMSAs)

Click the link on the right to download NCBI Conserved Domain Database hiMSAs, from which MAPGAPS can construct large MSAs as input to BPPS and DARC.

NCBI taxonomy dump ftp site

The taxdump.tar.gz and accession2taxid/prot.accession2taxid.gz files are required by the addtax program (see SOFTWARE). 

NCBI non-redundant protein sequence file ftp site

Download the fasta formatted nr.gz and pdbaa.gz files at this site for use as input to MAPGAPS and other programs.