The programs and licensing

The program package with the documentation listed above comes with a standard gnulicense. Link to the gnu organisation. You can download the whole package (version 2) here, or download and read manpages for selected ones on the list below (click on program name to go to man page).

Database expansion

Program	Short description
getseqs	Automated search and align0 realignment of global regions of blast hits.

RNA tools

Program	Short description
stdpair	Removes non-standard RNA pairs.
addparen	Inserts parenthesis structure lines.
extendstem	Extends RNA stems where possible.
support	Calculates which base pairs that have support.
shiftchk	Colors nucletide pairs different colors.

RNA format tools

Program	Short description
ct2col	Converts the ct format used by MFOLD to col format.
col2ali	Converts col format to ali format used by Rnaviz.
col2alis	Converts col format to several ali format files with color mask for each sequence used by Rnaviz.
col2ct	Converts col format to ct format.
col2seq	Converts col format to seq format.

General sequence tools

Program	Short description
unknown	Indicates non-standard symbols in alignment.
nogap	Removes gaps from sequences.
greppos	Takes out specified alignment positions.
grepcol	Takes out specified sequences from file.
joincol	Joins several col files.
colorpos	Indicate specific positions.

General format tools

Program	Short description
merge_head2col	Merge header to txt file and produce final col version of database.
gethead	Extract the headers from the col file.
txt2col	Convert a text alignment to col format.
col2txt	Converts col file to text file.
col2line	Converts col format to the more packable line format.
line2col	Converts line format to col format.
col2psalign	Makes postscript alignment file from col file.
col2txtalign	Makes text alignment file from col file.
gb2col	Converts GenBank file to col format.
col2fasta	Converts col file to fasta file.
blast2col	Converts blast result to col format
aln2txt	Converts aln format to txt format.

Coloring tools

Program	Short description
ali_shade	.
stem_shade	Colors stems green and loops blue..
stem_colors	Colors stems of alignment in different colors.
group_colors	Colors alignment with more pairingmasks different colors.
reliability_shade	Colors alignment according to reliability score of double or single stranded.
stem_variation	Uses first sequence as reference and colors alignment according to the differences.