Sentence examples for a reconciliation analysis from inspiring English sources

To infer the processes of gains and losses of Tas2rs across the bird phylogeny, we carried out a reconciliation analysis in NOTUNG 2.6 program (Chen et al. 2007) by comparing the species tree with the gene tree.

A simple reconciliation analysis performed on 20 representative species confirmed the topology agreement between gene and species trees (Additional file 1).

To evaluate the topology agreement and to highlight the importance of the amino acids under investigation, a simple reconciliation analysis was performed by GeneTree 1.3.0 [ 41].

For an event-based reconciliation analysis, we used JANE [ 63].

Since the computational complexity of the reconstruction problem is prohibitive when the number of gene transfers is large [34], we limited the Jungles reconciliation analysis to a maximum number of three gene transfers.

The reconciliation analysis identified a duplication at node 5 corresponding to this relationship (Fig. 3).

In order to elucidate evolutionary footprints, reconciliation analysis was performed with a species tree and an Argonaute gene tree.

The reconciliation analysis showed that for a relative small fraction of the gene families, larger gene family sizes in the extant pathogens F. graminearum and M. grisea resulted from expansions of ancestral or later gained gene families specifically occurring in these genomes (17% of the families in M. grisea and 16% of the families in F. graminearum).

Co-duplications may also be the result of undiscovered constraints at the genomic level (e.g. synteny), or an unknown systematic artifact of our gene reconciliation analysis that infers that unrelated genes duplicate or are lost at particular nodes.

The estimates of divergence dates argue for a more complex evolutionary history than estimated by reconciliation analysis.

For the internal modules, both ML and Bayesian analyses group the third A domain (D.3) of NPS2 Type V and the second A domain of the NPS1/SidC lineage together (yellow boxes), supporting a duplication at node 3 inferred by the reconciliation analysis (Fig. 3, see Additional files 3 and 6).