Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"

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