For genome alignment, it's hard to go past the MUMmer software suite. Chromosome alignment is very fast, typically a few seconds.
You might find the MUMmer SNP detection pipeline useful. Assuming you have want to align 2 chromosomes, in fasta files named chr1.fa and chr2.fa, start with nucmer:
nucmer --prefix=chr1_chr2 chr1.fa chr2.fa
Then run show-snps on the resulting delta file:
show-snps -Clr chr1_chr2.delta > chr1_chr2.snps
Sample output (first few lines):
[P1] [SUB] [P2] | [BUFF] [DIST] | [LEN R] [LEN Q] | [FRM] [TAGS]
24 A G 797603 | 24 24 | 5315120 5248520 | 1 1 chr1 chr2
53 . T 797633 | 29 53 | 5315120 5248520 | 1 1 chr1 chr2
759 C T 798339 | 45 759 | 5315120 5248520 | 1 1 chr1 chr2
You can then use SNP totals to measure genetic distance. One approach to this is described in:
Completion of the Genome Sequence of Brucella abortus and Comparison to the Highly Similar Genomes of Brucella melitensis and Brucella suis
which states in the methods section:
SNP totals were used as a measure of genetic distance for the neighbor-joining tree [Ps = (ΣSNP count/1,000)] construction with MEGA2.