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Special Forums News, Links, Events and Announcements Software Releases - RSS News Geneious 4.5.4 (Default branch)
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Old 01-28-2009
Geneious 4.5.4 (Default branch)
ImageGeneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as linear and circular DNA sequences, proteins, phylogenies, chromatograms, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, restriction analysis, contig assembly, access to biological databases at NCBI and elsewhere (PubMed, Nucleotide, PopSet, SNP, Structure, PFAM, etc.), BLAST, and more. It includes an API for creating your own plugins.License: Other/Proprietary License with Free TrialChanges:
This release fixes a couple of small bugs, including crash and performance bugs when assembling and viewing contigs.Image

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LEARN ABOUT DEBIAN

dotter

DOTTER:(1)						      General Commands Manual							DOTTER:(1)

NAME

       dotter - Sequence dotplots with image enhancement tools.

SYNOPSIS

       dotter [options] <horizontal_sequence> <vertical_sequence> [X options]

DESCRIPTION

	      Reference:  Sonnhammer ELL & Durbin R (1995). A dot-matrix program with dynamic threshold control suited for genomic DNA and protein
	      sequence analysis. Gene 167(2):GC1-10.

       Allowed types:
	      Protein	     -	    Protein DNA 	   -	  DNA DNA	     -	    Protein

	      Options:

       -b <file>
	      Batch mode, write dotplot to <file>

       -l <file>
	      Load dotplot from <file>

       -m <float>
	      Memory usage limit in Mb (default 0.5)

       -z <int>
	      Set zoom (compression) factor

       -p <int>
	      Set pixel factor manually (ratio pixelvalue/score)

       -W <int>
	      Set sliding window size. (K => Karlin/Altschul estimate)

       -M <file>
	      Read in score matrix from <file> (Blast format; Default: Blosum62).

       -F <file>
	      Read in sequences and data from <file> (replaces sequencefiles).

       -f <file>
	      Read feature segments from <file>

       -H     Do not calculate dotplot at startup.

       -R     Reversed Greyramp tool at start.

       -r     Reverse and complement horizontal_sequence (DNA vs Protein)

       -D     Don't display mirror image in self comparisons

       -w     For DNA: horizontal_sequence top strand only (Watson)

       -c     For DNA: horizontal_sequence bottom strand only (Crick)

       -q <int>
	      Horizontal_sequence offset

       -s <int>
	      Vertical_sequence offset

	      Some X options: -acefont <font> Main font.  -font    <font> Menu font.

SEE ALSO

       http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.

AUTHOR

       Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010

								     July 2010								DOTTER:(1)