| 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. |
All these files, with the exception of data.txt and smiles.tsv, can be automatically generated with turterra-build from a .fasta file containing the sequences you wish to analyse (use accessions of your choice as header), and a folder containing .pdb structures for homology modelling.
## Running turterra-build
Turterra-build uses [Muscle](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-113)(default settings) for sequence alignment, [FastTree](http://www.microbesonline.org/fasttree/)(default settings) for phylogenetic tree construction, [Modeller](https://salilab.org/modeller/)(250 models per sequence) for homology modelling, and Caretta for structure alignment. Turterra-build is run as follows:
```
Usage: turterra-build [OPTIONS]
Options:
--fasta. [required] .fasta file containing all sequences
to analyse, using accessions as headers.
--build-models / --no-build-models
Run modeller to construct homology models
using MODELLER v10.0. [default: False]
--build-alignment / --no-build-alignment
Build a multiple sequence alignment using
Muscle v3.8. [default: False]
--alignment Multiple sequence alignment. Required if
--build_alignment is false. [default: '']
--build-tree / --no-build-tree Build phylogenetic tree using FastTree
v2.1.10. [default: False]
--model-templates. Directory containing templates for homology
modelling in .pdb format. Required if
--model is passed. [default: '']
--num-threads. Number of threads used for homology
