slice_mercator_alignment - Extracts the corresponding subalignment from a Mercator multiple alignment

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

slice_mercator_alignment 1.15.9                   December 2015                      SLICE_MERCATOR_ALIGNMENT(1)

       slice_mercator_alignment from FSA 1.15.9

       Extracts the corresponding subalignment from a Mercator multiple alignment.

       slice_mercator_alignment - Extracts the corresponding subalignment from a Mercator multiple alignment

-h, --help
              show this message

       -D, --data <directory>
              path to map, genome and alignment files

       -M, --map <directory>
              path to map and genome files

       -A, --align <directory>
              path to alignment files

       -L, --lazy
              warn, rather than die, if the subalignment can't be obtained

       -U, --truncate
              truncate unmappable sequence (rather than skipping) and show truncated subalignment

       -s, --stockholm
              use and display Stockholm-format alignments with conservation statistics (default is multi-FASTA)

       -0, --zerobased
              coordinates are 0-based (default is 1-based)

       -o, --halfopen
              end coordinate is open, i.e., [start, end)

       Assumes that coordinates are 1-based and fully-closed, therefore representing the interval [start, end].

       If  requested,  unmappable  sequence  will be truncated to the mappable portion; note that the truncation
       will favor the beginning of the requested sequence.

       If  the  requested  sequence  is  on  the  -  strand,  then  the  corresponding  subalignment   will   be
       reverse-complemented.

slice_mercator_alignment [options] <genome><chromosome><start><end><strand>