What would your recommendations for the best MSA programs for comparing large nucleotide sequences of the same species?
My data set consists of 66 individuals from 11 populations. I will be using VariScan to scan for selection next, but need to realign each of the 21 chromosomes separately for each; population (6 individuals x 11 replicates), population pair (12 individuals in 5 replicates, excluding the outgroup), ecotype (30 individuals x 2 ecotypes), and all individuals together (66 individuals). To give you an idea of the size, chromosome 1 is ~26Mb, in a single consensus fasta sequence.
I was using GUIDANCE with the PRANK algorithm (commonplace in phylogenomic studies), but even on a high performance computing cluster, it took too long for one chromosome with only 6 individuals to make it a feasible approach. I am currently doing a test using MAFFT, but I have been warned it may have a sequence size limitation - it's currently running so we'll see.
Thanks in advance, and if I missed explaining anything, please let me know!