NAME

BS_ChromosomeDiff.pl

VERSION

Version 1.01

DESCRIPTION

This utility takes two versions of a chromosome and lists the differences
 between them. It will take note of added or deleted features, the addition or
 loss of subfeatures, changes in ORF translation, changes in feature sequence,
 and changes in annotation.

ARGUMENTS

Required arguments:

-F   --FIRST   : the 'original' chromosome
-S   --SECOND  : the 'variant' chromosome

Optional arguments:

-PT,   --PTRANSLATION : check ORF translations
-PA,   --PALIGN : make alignments for features with translation differences
-NS,   --NSEQUENCE : check nucleotide sequence differences
-NA,   --NALIGN : make alignments for features with nucleotide changes
-G,    --GROUP : sort results by 'feature' (default) or by change 'type'
-O,    --OUTPUT : html or defaults to txt
-h,    --help : Display this message