| sequences.fasta | A .fasta file containing all the sequences in the analysis, with the accessions specified in data.txt as headers. |
| sequence_alignment.fasta | A .fasta file containing an alignment of all sequences in the analysis, with the accessions specified in data.txt as headers. |
| smiles.tsv | A tab-separated file, with as header 'Name\tSMILES', and all compounds names in the analysis and their corresponding structures in [SMILES format](http://opensmiles.org/opensmiles.html). |
| structure_alignment.fasta | A .fasta file containing a structure-based sequence alignment of all sequences in the analysis, with the accessions specified in data.txt as headers. We recommend you create this file with [caretta](https://github.com/TurtleTools/caretta) through turterra-build. |
| structures | Directory containing structural (homology) models for sequences in the analysis in .pdb format. File names should have the format 'accession_model.pdb' for homology-modelled structures, and 'accession.pdb' for crystal structures. Accessions should match the accessions in data.txt. |
| tree.txt | A phylogenetic tree in newick format. Leaf nodes should be labelled with the accessions specified in data.txt. |