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For all samples, alignment was performed using bwasw [ 28], with default parameters.
For the HCV samples, alignment was performed against the entire pGEM genome with an HCV 1a strain insert, corresponding to the inserted fragments [ 6].
More information about the samples, alignment, variant calling and filtering, and annotation of the sequenced animal genomes is in Daetwyler et al. [ 28].
The StatAlign package - a Markov chain Monte Carlo (MCMC) sampler implemented in Java - samples alignment parameters, sequence alignments, tree branch lengths and tree topologies in order to infer both the alignment and the phylogenetic tree relating the input sequences [ 28].
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Analysis questions: Sample alignment: 1.
Firstly, a motorised x,y,z sample mount capable of holding an APD cryostat has been developed; this device is useful not only for initial sample alignment, but also in mapping a sample for the location of single crystallites.
A tool recently developed (Riddell et al. 2012) will allow more detailed examination of within-tree patterns and eliminate problems associated with sample alignment (with respect to stem axis).
The small relative difference of both scans comes from a discrepancy of sample alignment and the use of different samples.
These polarization-resolved SHG images were obtained without relying on any sample alignment or analyzer rotation before the detector.
The array also served as a visual indicator of sample alignment while remounting in a holder for MSI after CRM.
Bright field microscopy was used for all sample alignment and focusing in order to minimize the exposure of the sample to the laser beam.
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