Abstract
While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens) to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available). We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.
Highlights
The DNA-barcoding initiative (Hebert et al 2003) and Next-Generation Sequencing technologies have dramatically increased the amount of molecular data available for biodiversity studies
DNA barcodes obtained from several specimens in several species are compared to test whether intra- and interspecies diversity matches the accepted species hypotheses, which are generally based on morphological characters
One way to efficiently detect such discrepancies is to visualize the data with a phylogenetic tree and compare the phenotypes of the sequenced specimens in the order they appear in the tree
Summary
The DNA-barcoding initiative (Hebert et al 2003) and Next-Generation Sequencing technologies have dramatically increased the amount of molecular data available for biodiversity studies. While numerous standalone programs are available to visualize phylogenetic trees (e.g., FigTree (Rambaut & Drummond 2009); Treeview (Page 2002); MrEnt (Zuccon & Zuccon 2010);...) none of them offer, to our knowledge, the possibility to automatically display pictures associated to the sequenced specimens in a way that enables a direct comparison of a tree and hundreds of associated images In our case, this gap in the analytical workflow appeared when we started to accumulate barcoding data from the specimens preserved in the collection of the MNHN (Muséum national d’Histoire naturelle) and stored in its databases (Puillandre et al 2012). TreePics has been designed to automatically associate hundreds or thousands of pictures to a phylogenetic tree, using only a web browser
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