reverted PHI_2.4.pl to use -w instead of use warnings
fixed typo that broke tblastn searches
removed headers and blank lines from protein scoring matrices to match expected format
removed unneeded argument value conversion
Multiple changes made to get protein searches working again.
updated tree eps image height adjustment section to use the correct copy count variable, eleminated a redundant count of copies
fixed pre-multiple alignment size filtering
Major changes: swapped Mafft for Muscle, added FastTreeMP for tree building and left Treebest for converting tree to image
updated README
updated README
Added options to stop program after each stage
Added version flag and version info
adjusted output directory creation and handling of files with multiple queries. Testing needed.
finished input/output handling changes in last commit. All input types were tested and are working.
edited argument parser help text
edited argument parser help text
tree image size tweaks
edited README
Added the creation of a log file that stores the input command used. Added an argument flag to skip the formatDB and custom indexing step if they've already been run on the genome
edits to argument parser help text