corrected the emptying of the dict segments_on_target_genome; this reduced the number of fragmented genes, that were due to segments from previous genome staying in the dict

adapted to keep the orientation of the segments from the walks. added functions to better handle inversions

adapted the code to keep the orientation of the segments from the walks. added functions to handle oriented segments

adapted the code to use the options for the output files. changed every instance of 'clustal' to 'aln' in the code

changed when the output was writen in the output files, and changed the input of a function to adapt to changes in Functions.py

corrected the selection of target genomes when none are specified so that it doesnt take the source genome