TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.
BackgroundFigures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.ResultsTreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees.ConclusionsAlthough illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.
HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13 873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle based and easily accessible by a web interface (). As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.
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