Supplementary material for "Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain" by Nikunj Maheshwari, Lars S Jermiin, Chiara Cotroneo, Stephen V. Gordon and Denis C. Shields

INTRODUTION TO DATA FROM Royal Society Open Science (in review)

AUTHOR AND CONTACT DETAILSAuthor   Lars S JermiinAddress  School of Mathematical and Statistical Sciences, University of GalwayContact  [e-mail]     5 March 2024

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This README file pertains to research described in the following manuscript:

Maheshwari, N., Jermiin L.S., Cotroneo C., Gordon S.V., Shields D.S. 2024. Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain. Royal Society Open Science (in review).

The file outlines the content of a digital archive that contains a detailed account of how the phylogenetic analysis described in the manuscript was done.

The intention behind the archive was to make it possible to reproduce the research. By releasing the archive into the public domain, we hope to reach a suitable level of transparency and compliance with the FAIR principle in research data management. 

The archive centres on a file called 00_SUMMARY_OF_ANALYSIS.log. This file gives a step-by-step account of how a input file a 981 known and putative lanthipeptides was processed, leading to and two output files with 389 lanthipeptides.

The input file, which contains sequences of amino acids, is called:    ./01_Original_data/lanC977ID.fasta

and the output files are called:

   ./36_Annotated/lanC977ID_revised-26_ginsi_Annotated.fst   ./35b_IQTREE2_boot_ginsi/02_BIC/lanC977ID_ginsi_final.fst.BIC.treefile

Here, the first output file is a file of aligned residues with less reliable alignment positions removed in FASTA format. The second output file is the inferred phylogenetic tree in the Newick format (i.e., the one shown in the manuscript).

SOFTWARE USED TO PROCESS THE DATA IN THE ARCHIVE

MAFFT v7.453 (https://mafft.cbrc.jp/alignment/software/)

Clustal Omega v1.2.3 (http://www.clustal.org/omega/#Download)

AliStat v1.14 (https://github.com/thomaskf/AliStat)

R v4.3.1 (https://cran.r-project.org)

Homo v2.1 (https://github.com/lsjermiin/Homo.v2.1)

HomoHeatMapper v1.0 (https://github.com/ZFMK/HomoHeatMapper)

SatuRationHeatMapper v1.0 (https://github.com/ZFMK/SatuRationHeatMapper)

FOLDER AND FILE STRUCTUREThe full set of folders is given below:   ./01_Original_data   ./02a_MAFFT_linsi   ./02b_MAFFT_ginsi   ./02c_Clustal_Omega   ./03a_AliStat_linsi   ./03b_AliStat_ginsi   ./03c_AliStat_Omega   ./04a_MAFFT_linsi   ./04b_MAFFT_ginsi   ./04c_Clustal_Omega   ./05a_AliStat_linsi   ./05b_AliStat_ginsi   ./05c_AliStat_Omega   ./06a_SatuRation_linsi   ./06b_SatuRation_ginsi   ./06c_SatuRation_omega   ./07_Surplus_removed   ./08a_MAFFT_linsi   ./08b_MAFFT_ginsi   ./08c_Clustal_omega   ./09a_AliStat_unique_linsi   ./09b_AliStat_unique_ginsi   ./09c_AliStat_unique_omega   ./10a_SatuRation_unique_linsi   ./10b_SatuRation_unique_ginsi   ./10c_SatuRation_unique_omega   ./11a_Revised_data-20_linsi   ./11b_Revised_data-13_ginsi   ./12a_MAFFT_revised-20_linsi   ./12b_MAFFT_revised-13_ginsi   ./13a_Saturation_revised-20_linsi   ./13b_Saturation_revised-13_ginsi   ./14a_Revised_data-32_linsi   ./14b_Revised_data-19_ginsi   ./15a_MAFFT_revised-32_linsi   ./15b_MAFFT_revised_19_ginsi   ./16a_Saturation_revised-32_linsi   ./16b_Saturation_revised-19_ginsi   ./17a_Revised_data-36_linsi   ./17b_Revised_data-22_ginsi   ./18a_MAFFT_revised-36_linsi   ./18b_MAFFT_revised-22_ginsi   ./19a_Saturation_revised-36_linsi   ./19b_Saturation_revised-22_ginsi   ./20a_Revised_data-40_linsi   ./20b_Revised_data-26_ginsi   ./21a_MAFFT_revised-40_linsi   ./21b_MAFFT_revised-26_ginsi   ./22a_Saturation_revised-40_linsi   ./22b_Saturation_revised-26_ginsi   ./23a_Revised_data-41_linsi   ./24a_MAFFT_revised-41_linsi   ./25a_Saturation_revised-41_linsi   ./26a_Revised_data-44_linsii   ./27a_MAFFT_revised-44_linsi   ./28a_Saturation_revised-44_linsi   ./29a_AliStat_linsi   ./29b_AliStat_ginsi   ./30a_AliStat_linsi_masking   ./30b_AliStat_ginsi_masking   ./31a_AliStat_linsi_masked   ./31b_AliStat_ginsi_masked   ./32a_SatuRation_linsi_Final   ./32b_SatuRation_ginsi_Final   ./33a_Homo_linsi_Final   ./33b_Homo_ginsi_Final   ./34a_ModelFinder_linsi   ./34b_ModelFinder_ginsi   ./35a_IQTREE2_boot_linsi   ./35b_IQTREE2_boot_ginsi   ./36_Annotated

Most of the folders presented above include an input file, one or more shell scripts, one or more output files, and sometimes even a README file.

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