bioinformatics
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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 Note that this list also contains programs which have been replaced by extended projects we started later on. 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. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).
Software
GeneMark™ - Free gene prediction software
The GeneMark-P and GeneMark-E programs determine the protein-coding potential of a DNA sequence (within a sliding window) by using species specific parameters of the Markov models of coding and non-coding regions. This approach allows deliniating local variations of coding potential, therefore, the GeneMark graph shows details of the protein-coding potential distribution along a sequence. GeneMark is documented as the most accurate prokaryotic gene finder. GeneMark.hmm-P and GeneMark.hmm-E programs are predicting genes and intergenic regions in a sequence as a whole. They use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.
The UNAFold web server is currenly an amalgamation of two existing web servers: mfold & DINAMelt. The aim of this web site is to integrate the existing servers and to expand by developing algorithms and software that will provide new services to the scientific community. Created by Nicholas R. Markham Andrew Wright Leslie S.
mfold Web Server
InterPro protein sequence analysis & classification
InterPro, protein sequence analysis & classification InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool. Read more about InterPro
