get summary from last alignments

Question

[karthic]

Dear all,

I have alignment two large genomes using last. It has given me a maf output file. Is there any way to get quick summary of the alignment, say how much of genome1 is alignment to genome2??

Thanks, Karthic

[Fatima]

I haven't used last, but bioperl has percentage_identity function and supports maf format.

https://bioperl.org/howtos/AlignIO_and_SimpleAlign_HOWTO.html

PhastCons and VISTA seem to be able to "plot the percent identity between two aligned sequences along their length"

There are also other tools that can convert MAF to other formats: maf-convert, MafFilter, ...