PROJ_final.tab | Standard. Tab-delimited headers & predicted clades |
PROJ_final.txt | Standard. A prettier output of the above |
LEVEL_trace.tab | Standard. Table of HMM scores at each level, suitable for visualization in R |
LEVEL_result.tab | Standard. For the current LEVEL, tab-delimited headers & predicted clades |
LEVEL_result.txt | Standard. For the current LEVEL, A prettier output of the above |
FASTA/ | Standard. Folder containing fasta files and newick trees |
FASTA/MOD_predictions.fas | Standard. Query sequence file with predictions added like: "_{PRED:CLADE}" |
FASTA/MOD_control.fasta | Optional. Alignment of predictions fasta file and guide sequences |
FASTA/MOD_control.nwk | Optional. Maximum likelihood tree of the above |
FASTA/PROJ_reannotated.fas | Default. Query sequences file with annotations replaced with predicted ones, ordered by clade |
FASTA/PROJ_ordered.fasta | Optional. Aligned version of the above, still ordered by clade |
FASTA/PROJ_tree.nwk | Optional. Maximum likelihood tree of the above |
FASTA/PROJ_clade_CLADE.fas | Standard. The re-annotated file partitioned into separate clade files |
c-*/ | Standard. Clade/lineage subfolder for the hierarchical predictions |
Read_Me.txt | This file |