Create and Modify genome-wide alignments
Scripts to create alignments after deletion of gaps
requires Python>=3.6
chmod 755 completedeletioncode.py
completedeletioncode.py -f <fasta_filename> -p <percentage_of_deletion> -o <output_filename> -l <seq_wrap_length> -n [include non-variable sites or variable sites only]
or
python3 completedeletioncode.py [options]
Arguments in detail
-f Input multifasta file
-o Output prefix for multifasta file
-l Number of bases to be printed per line in output fasta [100]
-p Percentage for partial deletion, default [100] is for complete deletion
-n Set flag to print non-varaible sites too [False]
Script to extract upstream and downstream sequences for a specificed region
requires Python>=3.6
chmod 755 FS_Extractinator.py
FS_Extractinator.py -i <multi_fasta_filename> -o <output_prefix> -l <seq_wrap_length> -S <Start position> -E <End position> -f <size of up/down flanking the sequence positions>
Arguments in detail
-i Input multifasta file
-o Output prefix
-l Number of bases to be printed per line in output fasta [80]
-f Number of bases upstream and downstream flanking the Start and the End position. Default size is 1000
-S Start position of the region
-E End position of the region