Using the replicated RNAseq data and the DESeq2 software, we performed a differential expression analysis between the acaricide resistant (PSR-TK) and a susceptible (HS) strain of P. ulmi.
Although the clarity varies between spectrogram-generating software, one spectrogram produced by Reddit user M4nic_H3dgehog (and more or less successfully replicated using the same software by us) contains detailed, and very, very graphic images of what appear to be one or multiple women being tortured.
Subsequently unrooted phylogenetic trees were constructed with the neighbour-joining algorithm and p-distances model (1000 bootstrap replicates), using the MEGA3 software package [ 62].
The induction level of NtMMP1 mRNA after one hour of incubation with either P. syringae or A. tumefaciens were calculated from three independent biological replicates using the AIDA software.
Unrooted gene trees were reconstructed for the original MSA and each bootstrap replicate using the phylogenetic software ExaML [ 78].
The signals from probes on the chip corresponding to the same gene were normalized using the RMAexpress software [12] (also the replicates representing the same developmental stages were averaged.
Relative gene expression was estimated based on data from four biological replicates, using the relative expression software tool (REST 2009 V2.0.13, QIAGEN, Hilden, Germany) which is a dedicated standalone software for estimation of gene expression and statistical analysis.
All data were analyzed using SPSS 18.0 software (SPSS Inc., Chicago, IL) and replicated using the software Stata 12.0 (StataCorp LP, Texas, USA), considering a two-tailed level of P < 0.05 statistically significant.
The phylogenetic tree was constructed by the neighbor-joining method with 1,000 bootstrap replicates, using the MEGA 4.1 software, and revealed that all of these sequences were grouped together in one cluster, but separate from other bocaviruses (Figure 1).
We averaged coefficients of membership across the five replicates using the software CLUMMP 1.1 [ 62] and DISTRUCT 1.1 [ 63] was used to plot the graphical representation of this membership.
