Research
Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees
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* Corresponding author: Carlos Llorens carlos.llorens@uv.es
1 Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de València, Paterna, Valencia, Spain
2 Biotechvana, Parc Científic, Universitat de València, Paterna, Valencia, Spain
3 Departamento de Sistemas Informáticos y Computación (DSIC), Universitat Politècnica de València, Valencia, Spain
4 Área de Paleontología, Dpto. Geología, Universitat de València, Paterna, Valencia, Spain
5 Centro Superior de Investigación en Salud Pública (CSISP), Valencia, Spain
6 CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
Biology Direct 2009, 4:41 doi:10.1186/1745-6150-4-41
Published: 2 November 2009Additional files
Additional file 1:
LTR retroelement phylogeny. Inferred based on pol using the 268 LTR retroelements used in this study. This tree includes information about names, Genbank accessions and hosts of all LTR retroelement taxa used. By clicking on each OTU in this tree, the user can download a GyDB file or Genbank accession of the requested element from GyDB or NCBI, respectively.
Format: ZIP Size: 224KB Download file or display content in a new window
Additional file 2:
Comparative analyses. Presented through an Excel file divided into four sections; AF2A) C-terminal module of CoDi-A-like Ty1/Copia INTs with significant similarity the chromodomain consensus; AF2B) hits of similarity using different core sequences of DrFV-1 as queries against HMM searches at GyDB; AF2C) phylogenetic networks; AF2D) GPY/F module multiple alignments between Bel/Pao and Ty3/Gypsy LTR retroelements.
Format: ZIP Size: 554KB Download file
Additional file 3:
Network markers and graphs. Excel file containing five sections; AF3A) guide file summarizing all markers; AF3B) bipartite multigraphs between distributions and PAM-like markers; AF3C) bipartite multigraphs between retroelement phylogeny and PAM-like markers; AF3D) summary of non-redundant MCs; AF3E) Phenotypic neighbors' network.
Format: ZIP Size: 1.3MB Download file
Additional file 4:
Building multigraphs. Zip-file containing all notebooks (Mathematica files) needed to visualize or reproduce graphs shown in this study. This is presented as a mini-web site containing three folders and two HTML files. Opening the HTML file called "Index.html" and following the steps summarized therein users can reproduce the analyses using Mathematica 7.0 or simply visualize them using the freely available Mathematica Player.
Format: ZIP Size: 1.2MB Download file or display content in a new window