Sentence examples for using the default alignment from inspiring English sources
Burrows-Wheeler Aligner (BWA) version 0.7.5a-r405 [ 97] was used to align the unprocessed Illumina reads to the EST library using the default alignment stringency.
Parameter selections: All test runs were performed using the default alignment parameters and the options -quiet, -outfile, -keyval, -noenergy unless specifically mentioned.
All the other multiple alignments were generated using the default alignment parameters including the Matrix-GONNET 250 and Gap Open Penalty -10.
Preliminary alignments of rps4-trnS and trnL-F (trnL intron + trnL-F spacer) data were obtained using the default alignment parameters in Clustal X [ 71] followed by manual adjustments.
As part of the phylogenetic analysis, all the alignments were performed with ClustalX 1.83 using the default pairwise alignment parameters (Gap Opening = 10.0, Gap extension = 0.1, Gonnet 250 protein weight matrix).
To analyse the relationships of autophagy-related genes identified in N. tabacum with that in A. thaliana and O. sativa, a multiple sequence alignment of ATG protein sequences was conducted with Clustal X ver. 1.81 program using the default multiple alignment parameters.
The programs were run using the default options for protein alignment, except for Mafft and Muscle.
The identified Trs120, Trs130, and Trs65 proteins were aligned by clustal [ 42], using the default settings for slow/accurate alignments (gap penalty of 10, gap extension cost of 0.2, 30% delay for divergent sequences, 4 space gap separation distance, without end gap separation, with residue-specific penalties, and using the Gonnet series protein weight matrix).
The coding sequences were aligned using the codon model of PRANK software (100701 version) using the default options [ 52], and alignment gaps were deleted manually.
A maximum-likelihood phylogeny was estimated from this edited alignment using the default parameters of RaxML-HPC2 [ 99] as implemented at the CIPRES Science Gateway [ 100].
Using the default settings of bwa the alignment against the HMP database was performed with 19 k-mers, while Kraken utilizes 31 k-mers.
