Dear Fahim,

Yes, absolutely. The best program to do this is chromevol. This applies a complex maximum likelihood approach to fit your chromosome data according to different chromosomal evolution events, e.g. chromosome fusion.

It is really essential because cytogeneticists brought this entirely erroneous thinking of the 'base number' since the 1920's, often concluding that either the smallest number or the most common number is the ancestral number. But in fact what matters is chromosome numbers in outgroups. And if you want to infer properly the ancestral chromosome number of a clade of interest, you should make sure to have a good sampling of outgroups.

I recommend to read the following two papers from my excellent colleagues.

Sousa, A., Cusimano, N., & Renner, S. S. (2014). Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae). Annals of botany, 113(4), 669-680.

Cusimano, N., Sousa, A., & Renner, S. S. (2011). Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by ‘x’. Annals of botany, mcr302.

You may also want to contact them if need more specific help with the software.

Best wishes

Guillaume

Well, ok for likelihood statistic estimation models, but please keep distinct the concept of basic chromosome number (x), and inferred ancestral basic chromosome number (p)!

For this aim, you can look at my review

Peruzzi L., 2013. "x" is not a bias, but a number with real biological significance. Plant Biosyst. 147(4): 1238-1241.

I might not know something important about peculiarities of chromosome evolution, but problem of searching ancestral state seems to me exactly fit the parsimony methods (McClade or Mesquite programs do this). By the way, you do not need time, just branching order. And you can say that species is basal only relatively to some group, it does not necessary preserve ancestral state of character