I would like to get the percentage of similitude of two genomic sequences, the supercontigs are obtained from:
(the above is just an example), the problem that I have is when I want to use the tool known as MultiPipMaker http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker/?
this tool allows to upload two DNA sequences in FASTA format and returns the similitude between the secuences. The issue that I have is that when the sequences are too big (> 4 Mb) the results appears with an error, saying that the blastz CPU time limit exceeded. The question that I have is how I can get the percentage of similitude with this type of tool? It seems that it cannot hold large sequences, even though in its papers it says the opposite.