BIOSERVER home page. GenoCAD: CAD Software for Synthetic Biology. PredictProtein - Structure Prediction and Sequence Analysis. Information Génomique et Structurale - CNRS UPR2589. Phylogeny.fr: Home. Mfold Web Server. GeneMark™ - Free gene prediction software. The GeneMark-P and GeneMark-E algorithms determine protein-coding potentials, the values of a posteriory probability of protein coding in a DNA fragment in six possible reading frames. The six frame GeneMark graph shows details of the protein-coding potential distribution along the sequence. The GeneMark.hmm-P and GeneMark.hmm-E algorithms predict prokaryotic (P) and eukaryotic (E) genes in a sequence as a whole.
The algorithms use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) algorithms identify the maximum likely parse of the whole DNA sequence into protein coding genes (with introns in E case) and intergenic regions. * "P" stands for "Prokaryotic" "E" stands for "Eukaryotic" "S" stands for "Self-training" For more information see Background and Publications.
Genome Browser. Software. This page lists all biological software that has been developed by Ben Stöver and Kai Müller. Note that this list also contains programs which have been replaced by extended projects we started later on. LibrAlign LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data TreeGraph 2 TreeGraph 2 is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree.
SeqState Primer design, sequence statistics, and indel coding according to various schemes PhyDE System-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data Parsimony and likelihood ratchet analyses with PAUP* TreeGraph Automated drawing of phylogenetic trees using an extensible tree description format IndelCoder Precursor of PRAP2. The command-line precursor of PRAP. QuickAlign Alignment editor for Macinthosh computers GRate. ApE- A plasmid Editor. Gatekeeper will report that the application is damaged and will prevent ApE from running. You have to go to System Preferences > Security and Privacy > General.
Check "Allow software downloaded from anywhere" to allow ApE to run. Appearntly, right click on ApE and select "Open" will not work to bypass Gatekeeper on all systems. Or use a command line function to change the quarantine attributes. I may need to put ApE on the Apple store and start charging for it to get around this in the future.
The current Mac version has a bad bug on Mavericks. Click here to make a voluntary donation in support of ApE. Get older versions Click the icons at the top of the page for the latest version (version 2.0.x is out of alpha testing) You can now export genomic regions from Wormbase directly: In the upper right drop-down menu button, select "Download Track Data". Alternatively, you can export a genomic region (from the genome viewer) as a FASTA formatted file (using the menu on the upper left). ApE-A-plasmid-Editor - How do I do...? ImageJ. Tutorials and Examples.