Output

The results of mga are written to a number of files whose prefix can be specified by option -o. The following files may be generated:

$\mathit{prefix}$.summary

This file contains the parameters used during the computation, a description of the sequences and a short statistics on the number and length of the various regions.

$\mathit{prefix}$.align

This file contains the data of the alignment. By default, only the positions of all matches, aligned and unaligned gaps are given. This results in a short output which is useful for getting a brief overview of the structure of the alignment. The actual sequence data of the matches and aligned gaps are presented if requested using options -match / -bl and -clustalw / -msascript / -greedy / -xdrop.

$\mathit{prefix}$.reg$\mathit{X}$

These files contain the sequence data of all aligned regions and matches in FASTA format. There will be a file for every continous region number X. The files will only be created if option -alignedseqs is specified.

$\mathit{prefix}$.gap$\mathit{X}$.seq$\mathit{Y}$

These files contain the sequence data of all unaligned gaps in FASTA format. There will be a file for every gap number X and every sequence number Y. The files will only be created if option -gap is specified.

$\mathit{prefix}$.chain

This file contains all chained matches and is generated by option -chain. The file can, for example, be parsed by a graphical user interface that visualizes the backbone of anchors and computes alignments of short gaps on demand.

$\mathit{prefix}$.xml

This file contains all information in a structured way using XML-format. It can be used to postprocess the output of mga, e.g., to generate HTML pages containing the alignment. This is demonstrated by mga2html.pl which is included in the distribution.

If option -o is not specified the output will be written to stdout. This does not work for all options, e.g., option -gap requires option -o to be present.