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

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