ViennaNGS::BamStat extracts both qualitative and quantitative information from BAM files, i.e. the amount of total alignments, aligned reads, as well as uniquely and multi mapped reads.
Nevertheless, the program can also be used to identify recombination between sequences in the data set, although it might underestimate the amount of recombination in alignments where the donor and recipient are closely related [ 65].
In particular, varying the amount of gaps in the alignment had an impact.
The initial step of the scoring algorithm is to measure the amount of information in the alignment of one side of the junction read.
The amount of gap in an alignment was determined as a percentage, in the following manner.
We define the score of an alignment segment to be: (9) Here, q i and d i denote the i-th segments of series q and d, respectively, s i is the amount of stretching in the alignment of the i-th segments, a i is the amplitude difference, and cor is the Pearson correlation.
X-ray results for heat set fibres suggested both an increase in the amount of crystallinity, and in crystallite alignment.
The memory savings are proportional to the amount of missing data in the alignment (Izquierdo-Carrasco et al., 2011) RAxML offers options to conduct fast and more superficial tree searches on datasets with tens of thousands of taxa.
We present and implement a generally applicable mechanism that allows for reducing memory footprints of likelihood-based [maximum likelihood (ML) or Bayesian] phylogenomic analyses proportional to the amount of missing data in the alignment.
