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.

Comments, questions, etc., email gorodkin@genome.ku.dk.

Last updated March 26th, 2007 by Jan Gorodkin