Sentence examples for using the count software from inspiring English sources
Ancestral gene content evolution of mitochondrial genomes was reconstructed using the Count software [ 53].
The most parsimonious scenario of gains and losses along the branches of the tree was calculated using the Count software [ 90], under Dollo parsimony, which does not allow parallel gains at the same site.
The evolutionary scenarios were reconstructed using the Count software with the same parameters as used for Archaea and the ribosomal protein phylogeny [ 39] as the guide tree topology (Table 3).
As revealed in the following gene evolutionary analysis using the Count software [ 72], considering the significant contribution of HGT events to the conserved unique genes, the uniqueness of the PAH-degradation genes identified only in the PAH-degraders might be explained by gene loss during evolution of the PAH-degrading phenotype under selection.
The gain and loss of the PAH-degradation gene groups (a total of 23 groups) was assessed using the Count software [ 72] based on the PAH-degrading genes matrix across the genus Mycobacterium (Additional file 4: Table S13 and Additional file 5: Table S14).
FISH spot counts were performed on maximum projections from z-stack images using the counting software in Nikon Elements.
Cid spot counts were performed on maximum z-projections from z-stack images using the counting software in Nikon Elements.
The number of GFP spots per nucleus was counted manually from maximum z-projections from z-stack images using the counting software in Nikon Elements.
In this study, we used the Count software package [ 8] to investigate the impact of model complexity on robustness and stability.
Quantification of the number of reads that exclusively mapped to genes with bovine Ensembl IDs was performed using the HTseq-count software package.
Automated colony counting was performed on imaged plates using the BioSpot counting software (BioSpot Academic Software Version 5.0, Cellular Technology Limited/CTL) set to parameters in Supplementary Table S2.
