Sentence examples for alignment files were from inspiring English sources

DNA sequences were aligned using ClustalX v1.8 [ 46], and the alignment files were saved as the input files for estimation of synonymous (Ks) and non-synonymous (Ka) substitution rates using K-estimator 6.0 [ 47, 48].

The alignment files were parsed for the reads where one mate is aligned to human chromosome and another to HPV.

Reads were aligned to the Arabidopsis genome (TAIR10) first using Tophat, and then the resulting alignment files were used to assemble transcripts.

Resulting bam alignment files were then processed with samtools 1.351 to produce mpileup files.

SAM alignment files were further processed to create pileup files using the SAMtools package (Sequence Alignment/Map format tools, [40], http://samtools.sourceforge.net/).net/

Syntenic alignment files were downloaded from UCSD genome browser (http://genome.ucsc.edu .Polymorphism data of D. melanogaster 5' regulator region were collected from a worldwide collection of lines: OK17, HG84, Z s)56, Z s 30 from Africa; yep2, yep10, yep25 from Australia; 253.4, 253.27, 253.30, 253.30 and 253.38 from Taiwan.

Alignment files were converted in phylip format.

Individual gene alignment files were concatenated using Phyutility [ 105].

Multiple sequence alignment files are available upon request.

All alignment files are available from the authors.

Alternatively, BAM alignment files are supported as input (Fig. 1).