added creation of fasta file containing copies larger than (query_len * filter_multiple) if filter_multiple is used
added check for successful creation of MSA and error message if it was not
added check for another uninitialized variable giving warnings
implemented a sequence shuffle and split for input files for multiple alignment containing >800 copies, resulting in groups of ~400 copies each. MSA and trees are made for each group
added python functions for sequence retrieval and standardization
fixed typos/minor bugs in new code from last commit
fixed missing closing brace from block edited in last commit of PHI_2.4.pl
set correct query_seq length and pass to standardize_flanks function
removed errounous setting of seq_len I forgot to remove in last commit
still tweaking new python functions
new python functions now working properly
new python functions now working properly
fixed wrong flank path use in some cases
move counter inside loop
added missing setting of query for directory input with files containing multiple individual queries
return group size from split function to use for adjusting tree image size
doubled tree image margin