Additional file 2 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

Comparisons with commonly used GI finding software. A tab-delimited text file containing comparisons between xenoGI and four other commonly used GI finding programs: SIGI-HMM, IslandPick, IslandPath-DIMOB, and Islander. These were done using validation ranges from the same five species used for in Table 1 and Additional file 1. Included are data for base-wise coverage and the proportion of validation ranges covered by a single predicted island. (TSV 0.834 kb

Additional file 3 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

Resource usage of xenoGI. Plots of RAM usage, user time and wall clock time for up to 40 strains running on 50 processors. (PDF 5 kb

Additional file 1 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

A more detailed description of the correspondence between xenoGI islands and validation islands. A tab-delimited text file containing each validation range used in the five species we looked at. Includes the assemblies used to compare with each strain and the tree. For each validation range gives the base-wise coverage, the amount of extra coverage, the number of overlapping xenoGI islands and any comments. (TSV 6 kb

biolog

Biolog profiles of engineered strain

1_Data_integration

R Script to load input files and collate into a single matched data frame containing fitness, growth rate, and genetic and biolog distance dat

3_PLSregression_&_correlations

Script to perform ANOVA testing for mutation effect variation over different recipient strains and to perform partial least squares (PLS) regression and plot contribution of independent variables to each componen

2a_Recipient strains on Broad phylo

R Script to identify engineered strains in context of broader E. coli phylogen

fitness_estimates

Fitness estimates of engineered strain

2_mutation_effect_ANOVA

R Script to perform ANOVA to: (i) examine variation in effect of each mutations over strains, (ii) examine variation in average effect of mutations per strain, and (iii) determine average effect of each mutatio