Boxshade program

Read more. Free Software Foundation! From Free Software Directory. Jump to: navigation , search. Licensing License. Verified by. PRE NB!! MSF input. We can't actually think why anyone would use this format now,. MSF files are more useful generally. Possible options depend on the graphics adapter used. SYS previously. Possible character renditions are reverse, bold,underlined, blinking etc.

Some of the formats above offer the possibility of scaling the characters and of rotating the plot. Character size has to be entered in 'point' units. When creating multi-page output, all pages are contained in a single output file. Sequence numbering Starting with version 2.

The numbers are printed between the sequence names and the sequence itself. Since most of the input-files either use no numbering or number the first position in the alignment always with a "1" and that does not necessarily reflect the numbers within the original sequence , the user is asked to enter the starting position for each sequence.

Boxshade starts with the value entered for the leftmost position and continues numbering every valid symbol, skipping blanks, '-','. Default parameters Several people using previous releases of BOXSHADE pointed me to the need of having default parameters for the various questions asked by the program. Copy the entire set of sequences to the clipboard. Paste the protein sequences in the large text box. Make sure ClustalW 1.

Leave all the other parameters as they appear, but notice the range of other possible options on this page. Click on the grey submit button to start the alignment. Step 3: After a short delay you will now be presented with the results page for the alignment of these four protein sequences.

Feb 7, Initial commit. Apr 28, Feb 15, View code. Input formats pyBoxshade supports a number of different input formats; it uses the BioPython library for reading aligment files, and can therefore read most of the formats supported by that library.

Output formats pyBoxshade provides four types of output, those I thought would be of most use: PS PostScript files for printing directly or further conversion. This format can first be viewed on screen, then saved as an image file. In the latter case it is possible to make a larger image using a large font and shrink this image down to the required size.

ASCII output showing either the conserved residues or the varying ones others as '-'. Shading strategy similarity to consensus or single sequence The shading algorithm used by BOXSHADE and hence by pyBoxshade is completely configurable by the user, and is not based on any specific mutational table. Consensus display pyBoxshade offers the possibility to create an additional line holding a consensus symbol.

Sequence numbering There is the possibility to add numbering to the output files. Marker line pyBoxshade has the ability to print a marker or ruler line over the sequence alignment. Binaries Binaries are available for MacOS tested on Releases 5 Only minor changes Latest. Packages 0 No packages published. You signed in with another tab or window.