How to do whole genome sequence alignment in R or Ruby/C++, any good language?
I think you incorrectly identified what type of analysis you want.  You mention that you have numerous sequences in a fasta file (you mention at least 60,000) that need to be aligned to a single genome.  So your not doing a pairwise alignment, your aligning DNA sequences to a reference genome.  The fastest known algorithm for this is burrow-wheeler transformation mappings which can be accomplished with tools such as bowtie, bowtie2, BWA, etc...

I'm assuming your experimental design is something like this: You have sequencing data from a number of tissue samples with half or some number of samples being a disease state, the other being normal.  So you want to create alignment files for each sample, and than determine where these alignments differ.

After alignment, you will need to create a variant file (VCF) which can be accomplished using samtools or GATK.  The VCF file will give you all bp locations with alternative alleles from your reference genome.  Which seems to be what your looking for.

Citations that could be useful:

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509

Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

https://www.broadinstitute.org/gatk/about/cited-by

The last url contains 145 publications that used GATK to look at population-scale variant differences.  These publications could be very useful to see how other papers have accomplished variant discovery for the use for scientific inference.

For User137 - since I can't comment on this board yet; you want to use a program called muscle.  There is an MS-DOS version and it can align short sequences extremely fast.