Input files follow commonly used formats: Newick format for the possibly multifurcating species phylogeny, Fasta format for alignments and the syntax used by Rogozin et al. (2003) for intron tables.
While this is the case for quantifications, which are made available individually at the gene, transcript and exon level, the BAM format is used as an output format for alignments.
The resulting sequences were formatted for alignment in the UCSC genome browser.
By default, Bowtie 2 (Langmead and Salzberg, 2012) is used, but users can change to any other short-read alignment algorithm that uses FASTQ/FASTA formats for read input and SAM/BAM formats for alignment output.
The set of plant viruses and the set of hsa-miRs were FAST formatted for alignment with Basic Length Alignment Sequence Tool for nucleotide-nucleotide matching (BLAST+ 2.2.25+), hosted by the National Center for Biotechnology Information (NCBI), and performed the BLASTN in a local server.
The output BAM file, a standard format for sequence alignment, generated by a short read aligner may be created in different locations, or the output may not be stored in BAM at all.
The necessary NEXUS file format for the alignment (input) file was generated with the file conversion option available within the DAMBE program [ 84].
FASTA is the most widely used format for sequence alignments and is output by most alignment programs.
We wrote our own Extractor (for the FASTQ files) and Analyzer (for summarization), and invoke the tool (SAMtools, http://samtools.sourceforge.net/samtools-c.shtml) for the (binary) Sequence Alignment/Map format (for multiple alignments) used by the Sanger Institute.
With the surge of NGS data, this came to include the SAM format for sequence alignments.
The BAM (Binary Alignment/Map) file format [ 9] is a generic and highly compressed format for storing alignments.
