This is the command delta2maf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
delta2blocks - extra tool for mummer from patch of mugsy to sort alignments
delta2maf - extra tool for mummer from patch of mugsy to sort alignments
SYNOPSIS
delta2blocks [options]<deltafile><refID><qryID>
delta2maf [options]<deltafile><refID><qryID>
DESCRIPTION
-h Display help information
-q Sort alignments by the query start coordinate
-r Sort alignments by the reference start coordinate
-w int Set the screen width - default is 60
-x int Set the matrix type - default is 2 (BLOSUM 62), other options include 1 (BLOSUM 45)
and 3 (BLOSUM 80)
note: only has effect on amino acid alignments
Input is the .delta output of either the "nucmer" or the "promer" program passed on the
command line.
Output is to stdout, and consists of all the alignments between the query and reference
sequences identified on the command line.
NOTE: No sorting is done by default, therefore the alignments will be ordered as found in
the <deltafile> input.
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