jplace_analysis

Scripts for parsing and analyzing jplace files

jparse_int_leaf

takes a jplace files and counts the number of internal placements and leaf placements on the tree

cog_func_placement_difference

takes all the jplace files from a metagenomic sample analysis and returns internal vs leaf placement for each functional class of cogs.

outlaw_code

one off code that should be avoided

Ideas

separate the cogs based on functional class (what functional family the cog belongs too) Check if inner placements are ambiguous or placed to specific level. as in, using ncbi tax id, what level is it identified at.