We used taxonomy from algae base [ 25].
The method uses the available taxonomic information as reference taxonomy for the known genomes and further uses this information to identify the taxon-specific genes unique to each taxonomic rank.
Finally, the 16S rRNA gene-sequencing method used to identify taxa of interest is limited because our identification was only as precise as the RDP attributed taxonomy.
The phylogeny matches both accepted taxonomy and a previous molecular phylogeny [ 18], validating both the predicted Stachybotrys proteomes and the OrthoMCL-based method used to identify homologs.
To check whether method co-occurrence is common, we randomly selected two behaviour change methods using data from the interventions coded in the HIV adherence meta-analysis (k = 31; for the coding manual, see http://marijndebruin.eu/meta/hivadherence/taxonomy).eu/meta/hivadherence/taxonomy
Figure 2 summarises the methods used to develop the COMMVAC taxonomy.
The lectures were designed to stimulate thinking and increase knowledge of appropriate issues, for example, contemporary taxonomies and methods used in the field, an introduction to the International Classification system of Functioning (ICF), and tools to identify rehabilitation needs and methods for evaluation [ 16, 17].
The first methods used for comparison were developed for other semantic taxonomies, mostly lexical taxonomies (Jiang and Conrath, 1997; Lin, 1998; Resnik, 1999).
Although this method was successfully used for taxonomy characterization at the species level, it was a time-consuming and expensive [ 5] process that required the application of exceedingly laborious data analyses.
We aimed to identify genomic regions conserved in the six species, predict evolutionary relationship between the analyzed bacteria, compare the predicted phylogeny to classification using microbial taxonomy methods, and identify the interspecies recombination events occurring within core genomes of the Harveyi clade.
