iGTP: A software package for large-scale gene tree parsimony analysis. - Ruchi Chaudhary; Mukul S. Bansal; André Wehe; David Fernández-Baca; Oliver Eulenstein (BMC Bioinform., 2010)

Algorithms for Rapid Error Correction for the Gene Duplication Problem. - Ruchi Chaudhary; J. Gordon Burleigh; Oliver Eulenstein (ISBRA, 2011)

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. - Ruchi Chaudhary; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2012)

Fast Local Search for Unrooted Robinson-Foulds Supertrees. - Ruchi Chaudhary; J. Gordon Burleigh; David Fernández-Baca (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. - Ruchi Chaudhary; John Gordon Burleigh; David Fernández-Baca (Algorithms Mol. Biol., 2013)

Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. - Ruchi Chaudhary; David Fernández-Baca; J. Gordon Burleigh (AlCoB, 2015)

MulRF: a software package for phylogenetic analysis using multi-copy gene trees. - Ruchi Chaudhary; David Fernández-Baca; John Gordon Burleigh (Bioinform., 2015)