Published June 22, 2020
| Version v1
Dataset
Open
Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"
Authors/Creators
- 1. Department of Medical and Biological Sciences, Oxford Brookes University, UK
- 2. Department of Ecology and Conservation Biology, Texas A&M University, College Station, Texas, USA
- 3. Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- 4. Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
- 5. Department of Biology, Texas A&M University, College Station, Texas, USA
Description
This repository contains data and information to reproduce the findings reported in the paper.
File descriptions:
- OTU_sequences.fasta – all Spiroplasma sequences that contained an OTU domain as predicted by PfamScan
- OTU_alignments.fasta – alignment of OTU domains performed using Mafft
- RIP_sequences.fasta – all Spiroplasma sequences that contained an RIP domain as predicted by PfamScan
- RIP_alignments.fasta – alignment of RIP domains performed using the HMMER package
- Spiroplasma_supermatrix.fasta – Fasta alignment of concatenated single copy Spiroplasma loci conserved across the investigated strains. Loci that showed signs of recombination were not included
- Spiroplasma_partitions.txt – Lists the loci that make up the Spiroplasma supermatrix
- Spiroplasma_partitioning.scheme.txt – Partitioning scheme employed in our Maximum Likelihood analysis of the supermatrix. This was the best fitting partitioning scheme as determined with IQ-TREE
- Protocol_1.pdf – Chloroform–Ethanol protocol used for extracting Spiroplasma DNA for sHy-Tx
Files
Protocol_1.pdf
Files
(937.6 kB)
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