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Analysis.md

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Analysis

How to reproduce the results reported in the paper

In the paper we perform an extensive benchmark and produce accessory analyses to assess the robustness and validity of Multistrap.

You can get the input data for the full dataset at: https://zenodo.org/records/7447443

We hereby provide the command lines necessary to reproduce the reported results. To run it on the real dataset, please download it and update the path of fasta, templates and pdb with the path you download the data to.

To run the main analysis present in the paper (uses untrimmed mTM-align MSAs to produce ME, ML and IMD trees): nextflow run main.nf -profile untrimmed_mTM

To modify the aligner or trimming to use you can do it with the following parameters:

  • align that determines the alignment method to use. It can be mTMalign, sap_tmalign, tcoffee
  • trimmer that determined the type of trimming of the alignment. It can be untrimmed or trimmal

To run the titration, you should run the pipeline like:

nextflow run main.nf -profile titration

To run bootstrap on titration trees:

nextflow run main.nf -profile titration_bootstrap

To compute extra statistics needed for the complete analysis shown in the paper, such as the calculation of NiRMSD, you can use the profile analysis.

nextflow run main.nf -profile analysis -msas <id.aln> -templates <id.template> -pdbs my_pdbs/*

The scripts to reproduce the figures and tables in the manuscript are available in the analysis folder.

The pipeline includes additional profiles that set default parameters values:

  • untrimmed_mTM that runs the standard analysis with the mTMalign untrimmed alignment
  • trimmed_mTM that runs the standard analysis with the mTMalign alignment trimmed by using trimal
  • untrimmed_3dc that runs the standard analysis with the 3d-coffee untrimmed alignment
  • trimmed_3dc that runs the standard analysis with the 3d-coffee alignment trimmed by using trimal
  • untrimmed_tc that runs the standard analysis with the t-coffee untrimmed alignment
  • trimmed_tc that runs the standard analysis with the t-coffee alignment trimmed by using trimal
  • titration that runs the titration analysis present in the paper; by default, it computes and uses untrimmed mTMalign alignment; if you wish to change the alignment method, you would have to change the align parameter and the input paths fasta and template
  • titration_bootstrap that runs the bootstrap for the titration-based trees; by default, it computes and uses untrimmed mTMalign alignment; if you wish to change the alignment method, you would have to change the align and the input paths fasta and template