Publications - Supplemental material

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BIOINF 15-037: The Expansion of Animal MicroRNA Families Revisited

Jana Hertel, Peter F. Stadler

ePoPE: efficient Prediction of Paralog Evolution

A dynamic programming algorithm designed to efficiently trace back the last common ancestor of a gene family and automatic annotation of gain and loss of its paralogs to the inner nodes of a given phylogenetic tree.

ePoPE is implemented in standard C programming language and available under the GNU General Public License.

Download: ePoPE_1.0.tar.gz

Installation, tutorial and usage information: ePoPE Software description


ePoPE output for the miRNA analysis in metazoa

Here you can download the results of ePoPE applied to miRNA alignments in 159 metazoan genomes. These are the results described in the corresponding publication [manuscript in review process].

  1. The table of all miRNA families i (rows). 1st column: miRNA family identifier according to miRBase, 2nd col: name of this miRNA family, 3rd col: Last common ancestor (LCA) of this family; Columns 4-139: species j. Each cell (i,j) contains the number of miRNAs of a certain family i in species j.
    miRNA-families-LCA-members.csv
    miRNA-families-LCA-members.xlsx
  2. Graphical (postscript) and test output of ePoPE for each miRNA family:
    ePoPE.metazoa.output.data.tar.gz [24MB]
  3. Mapping of species name and its abbreviation used in the alignments:
    Metazoa.tree.abbrv.species.csv