[BioC] Downloading Multiple Genome Alignments from UCSC Genome Browser

[Manuel Razo-Mejia [guest]]

I have been using the fantastic rtracklayer package to download the Conservation-track for several 3'UTR regions of different species. This has worked fantastically up to now without any problem.
But I'm also interested in accessing the 
multiz60way table that returns the MAF files with the multiple genome alignments for the same regions. Currently rtracklayer doesn't support downloading this type of files so I was wondering if anyone knows a way (not necessarily in the Bioconductor environment) to download this track for multiple locus in an automatic way.

 -- output of sessionInfo(): 

R version 3.1.0 beta (2014-03-28 r65330)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rphast_1.5            rtracklayer_1.23.20   GenomicRanges_1.15.41 GenomeInfoDb_0.99.26 
[5] IRanges_1.21.38       biomaRt_2.19.3        Biobase_2.23.6        BiocGenerics_0.9.3   
[9] BiocInstaller_1.13.3 

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.25.17     BatchJobs_1.2             BBmisc_1.5               
 [4] BiocParallel_0.5.18       Biostrings_2.31.20        bitops_1.0-6             
 [7] brew_1.0-6                BSgenome_1.31.12          codetools_0.2-8          
[10] DBI_0.2-7                 digest_0.6.4              fail_1.2                 
[13] foreach_1.4.1             GenomicAlignments_0.99.32 iterators_1.0.6          
[16] plyr_1.8.1                Rcpp_0.11.1               RCurl_1.95-4.1           
[19] Rsamtools_1.15.37         RSQLite_0.11.4            sendmailR_1.1-2          
[22] stats4_3.1.0              stringr_0.6.2             tools_3.1.0              
[25] XML_3.98-1.1              XVector_0.3.7             zlibbioc_1.9.0    

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