INRA Biometry and AI dept. Chemin de Borde Rouge BP 27 31326 Castanet Tolosan Cedex FRANCE
We present Carthagene, a new free marker ordering software. Essentially, Carthagene aims at keeping the best of MapMaker and JoinMap. Like MapMaker, Carthagene uses multipoint maximum likelihood estimations of distances. Like JoinMap, it can handle data made up of several distinct populations which may each be either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds and/or radiated hybrids. The criteria used to find the best ordering is always a true multipoint maximum likelihood criteria which is computed using an extended EM algorithm that performs orders of magnitudes faster than MapMaker/RHMap EM algorithms on backcross, RIL and RH data, without any loss of precision. In order to be able to find maximum likelihood orderings, Carthagene includes several algorithms. This goes from the traditional build/flips algorithms to more powerful ordering methods based on simulated annealing, taboo search and genetic algorithms. These algorithms have been applied eg. to three populations of doubled haploid data which lead to linkage groups with more than 60 markers. These algorithms do not only look for one single maximum likelihood order but also offer, like MapMaker 'compare' method, alternative orders with slightly lower likelihood. This gives an opportunity to assess the strength of the best order found. Finally, Carthagene offers two interfaces: a completely programmable MapMaker-like text interface wich includes a complete programming language and also a graphical interface that directly draws consensus maps. Carthagene currently runs on Unix-like operating systems (Solaris, Linux, IRIX) but a Windows based version is expected soon. For more information see CarthaGene web site.
Plant & Animal Genome VIII Conference Plant & Animal Genome VIII Conference