January 2010 - beg-evodevo@psb.ugent.be

[Beg-evodevo] [Fwd: Confronting Intelligent Design arguments directly in the scientific literature]
by Klaas Vandepoele 21 Jan '10

21 Jan '10

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[Beg-evodevo] Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
by Pierre Rouze 08 Jan '10

08 Jan '10

http://www.pnas.org/content/107/1/472.abstract?etoc from dear old Paterson ... -- Pierre ROUZE Bioinformatics / Senior Expert Scientist VIB Department of Plant Systems Biology Ghent University Technologie park 927, B-9052 GENT BELGIUM Tel :32.933 13694 Cell.Phone : 32.476 638 304 Fax :32.933 13809 pierre.rouze(a)psb.vib-ugent.be http://www.psb.ugent.be/bioinformatics ¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨ prediction is very difficult, especially about the future Niels Bohr

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[Beg-evodevo] Abstract | TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
by Klaas Vandepoele 08 Jan '10

08 Jan '10

http://www.biomedcentral.com/1471-2105/11/7/abstract TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses *Ben C Stoever* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> and *Kai F Mueller* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> /BMC Bioinformatics/ 2010, *11**:*7doi:10.1186/1471-2105-11-7 Abstract (provisional) Background Today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. A tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures. Results We developed TreeGraph 2, a GUI-based graphical editor for phylogenetic trees (available from http://treegraph.bioinfweb.info) It allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. The program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). Beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph 2 outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations.

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