Sentence examples for format the alignment from inspiring English sources

Jalview has been modified to format the alignment in a virologist-friendly way.

As its default output file format, the alignment phase uses maf format.

We used the samtools mpileup command to format the alignments in "pileup" format.

The corresponding tree can be exported as a text file in standard 'dnd' format, whereas the alignment can be exported in 'ClustalW' format.

The coordinates of these SNPs were converted into BED format, and the alignment data at the SNP coordinates were extracted with SAMtools mpileup60.

We stressed the benefits of using the "COG groups" format in the alignment of many networks.

The necessary NEXUS file format for the alignment (input) file was generated with the file conversion option available within the DAMBE program [ 84].

Second, the data exists in a specialized format, the Multiple Alignment Format (MAF; Supplementary Fig. S1).

The raw data in the fastq format, and the alignments and genotyping data from this study are hosted in the GigaScience Repository, GigaDB [ 43].

The output consists of the name and sequence logo of the highly-ranked database hits, along with the pairwise alignments (in consensus sequence format) and the alignment E-values (see Figures S4, S5, S6, S7, S20).

Optionally, verbose output can be switched on in order to retain full sequence information for novel alleles, including the alignment (bam format), pileup (pileup format) and consensus sequence (fastq format) obtained from mapping to the closest-matching locus variant.