Microbial Recombination with Population Structure

<p>This collection of data files contains, for each bacterial species:</p> <ol> <li>All raw genome sequence files.</li> <li>The core genome alignment obtained with REALPHY (this is the file with the .phy extension).</li> <li>A file with all SNP columns in the core genome alignment (the file name starts with columns_).</li> <li>A file listing all SNP types sorted from most to least common (the file name starts with snp_stats_)</li> <li>Two files containing the results of the pairwise analysis. First, a file with, for each pair, the histogram of SNP counts per alignment block (the file name ends in _histograms). And second, a file with the results of the mixture modeling (the file with the .pkl extension).</li> </ol> <p>In addition, for M. tuberculosis there is a subfolder with information about which strains have since been retracted from the database.</p> <p>&nbsp;</p> <p>The formats of these files are as follows:</p> <ol> <li>The raw genome sequence files are in FASTA format (.fasta or .fna).</li> <li>The core genome alignment is in PHYLIP multiple alignment format (.phy).</li> <li>The snp_stats file starts with a header line listing the total number of columns in the alignment with 1, 2, 3, and 4 different nucleotides. Each next line in the file corresponds to an observed SNP-type, sorted from most to least common. Each SNP line has the following columns:</li> </ol> <ol> <li>The total amount of genomic DNA associated with these SNP columns (associating each conserved alignment column to its closest SNP).</li> <li>The total number of occurrences of this SNP type.</li> <li>The number of strains sharing the minority allele.</li> <li>A bit-pattern describing the SNP type, with 1 for the strains sharing the minority allele, and zero for the others. The strains are sorted in the same order as in the PHYLIP alignment file.</li> <li>A list of all the strains sharing the minority allele.</li> </ol> <ol> <li>The columns_ file has one SNP per line, giving the position in the alignment plus the bit-pattern describing the SNP.</li> <li>The _histogram file contains, for each pair of strains, a histogram counting the number of 1Kb blocks with 0, 1, 2, etc SNPs. Note that these counts come from 1 kilobase sliding windows along the core genome alignment, sliding the window by 100 bases at a time, i.e. an alignment column will typically occur in 10 blocks.</li> <li>A pickle file with, for each pair, the results of the mixture modeling. &nbsp;Each line corresponds to a pair and has these fields: [spec1, spec2, div, Lpois, r_nomix, Lmix, rho, r, a, lam, mutpois, mutrecomb, cut] which correspond to:</li> </ol> <ol> <li>Name of strain 1.</li> <li>Name of strain 2.</li> <li>Their overall nucleotide divergence.</li> <li>The log-likelihood under a model assuming SNP counts form a simple Poisson distribution.</li> <li>The parameter of this fitted Poisson distribution.</li> <li>The log-likelihood of the mixture of a Poisson and negative binomial</li> <li>The fraction rho assigned to the Poisson part of the mixture.</li> <li>The parameter of the Poisson component.</li> <li>The exponent a of the negative binomial component.</li> <li>The second parameter (lambda) of the negative binomial.</li> <li>The estimated total number of mutations in the Poisson component.</li> <li>The estimated total number of mutations in the negative binomial component.</li> <li>The value at which the likelihood of negative poisson component starts exceeding the likelihood of the negative binomial component.</li> </ol> <p>&nbsp;</p> <p>In addition, for the human data we provide a PHYLIP multiple genome alignment and a file with all SNP columns.</p>