Hmmm great link Rahul, You can also try Mugsy: fast multiple alignment of closely related whole genomes http://bioinformatics.oxfordjournals.org/content/27/3/334
In my works, I have also used BWA-SW, BLAT and LASTZ. However, LASTZ is not well-suited for aligning to many chromosomes at once. Whereas, the BLAT is difficult as PSL to BAM conversion is imperfect in it.
I would recommend python and lower level language C because of easier syntax and simple oops approach. Moreover, I do a lot of boinformatics programming, but I don’t use any of the “Bio*” projects, as they never seem to have much that is of use to me, and what little is useful to me is easier for me to code myself than to install any Bio* project and deal with its idiosyncracies.
Python is beating all others https://towardsdatascience.com/the-most-in-demand-skills-for-data-scientists-4a4a8db896db