ALES - A Lineage Evaluation SystemAles is a tool for visualizing and analyzing cell lineages. It allows the display, evaluation and comparison of cell lineages with the aim of identifying key events underlying development. Ales introduces metrics that locate putative developmental events. In addition, artificial cell lineages can be generated according to a range of models, in order to provide a basis for statistical analysis of lineage metrics and to test hypotheses about lineage evolution. More details about the lineage metrics and the models to generate artificial cell lineages can be found in (Braun et al., 2003).
Caenorhabditis elegansWe have used Ales to analyze the V6L.pap neuronal sublineage of the nematode Caenorhabditis elegans (Braun et al., 2003). Putative developmental events have been inferred using the tool's lineage metrics and have been compared to known developmental mechanisms. Furthermore, random cell lineages with the same cellular composition as the V6L.pap sublineage were generated and analyzed using Ales. Comparison to the real lineage allowed us to get insights into the evolution of the developmental program.
Ales has also been used in the analysis of the complexity of the full C. elegans cell lineage, as well as those of two other nematodes and an ascidian (Azevedo et al., 2005). The evolutionary simulations used additionally in this analysis were carried out using Les, a command-line tool based on Ales.