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The genetics software gathers patient data, pairs it with other data and tells them the results.
Statistical genetics software packages for linkage analysis have their own unique constraints on the size and shape of the pedigrees they can process.
Hardy-Weinberg equilibrium of alleles was tested using PROC ALLELE in the SAS genetics software package (version 9.1, SAS computing).
Haplotype analysis was performed using population genetics software Arlequin 3.1 [ 10].
Data analyses were carried out with GeneSpring version 4.2.1 (Silicon Genetics) software, including filtering, K-means and hierarchical clustering.
File conversions, to allow the use of various population genetics software, were accomplished using PGDSpider v. 2.0.5.1 (Lischer and Excoffier 2012).
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All phylogeny trees were created with full length sequences of representative serine threonine kinases from different organisms with help of Neighbor Join (NJ) method [26] using "MEGA 4", a molecular evolutionary genetics analysis software [41].
Phylogenetic trees were generated by comparing the amino acid sequence of nine pAPEC-1-associated virulence genes with those of related sequences of other bacteria obtained from the GenBank database by neighbor-joining (1,000 replicates) using molecular evolutionary genetics analysis software version 4.0 (MEGA4) (http://megasoftware.net/).net/
Handling of microarray results and statistical comparisons were performed with GeneSpring (Silicon Genetics, 2004) software.
Sequence alignment was done using the molecular evolutionary genetics analysis software version 5 (MEGA5) [ 27].
All phylogeny trees were constructed using "MEGA", a molecular evolutionary genetics analysis software [ 54].
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