:tocdepth: 3 .. _guppy_indep_c: ======= indep_c ======= `indep_c` calculates the independent contrasts of pqueries. :: usage: indep_c [options] placefile[s] Options ======= --pp Use posterior probability for the weight. -o Specify the filename to write to. --out-dir Specify the directory to write files to. --prefix Specify a string to be prepended to filenames. --csv Output the results as csv instead of a padded matrix. --leaf-values Name of CSV file giving values for the leaves of the tree. Details ======= This is an implementation of the "independent contrasts" method of `(Felsenstein, 1985)`_. Assume we have the following pair of placements on a simple tree:: {"tree": "((A:2{0},B:9{1}):7{2},C:5{3},D:1{4}):0{5};", "placements": [{"p": [[0, -1309.83, 1, 1, 10]], "n": ["read1"]}, {"p": [[1, -1309.83, 1, 2, 10]], "n": ["read2"]} ], "version": 3, "metadata": {}, "fields": ["edge_num", "likelihood", "like_weight_ratio", "distal_length", "pendant_length" ] } And that ``ic.csv`` is a (possibly partial) list of tip values as follows:: A,3 B,0 D,1 Then, a run of ``indep_c`` will give you the maximum likelihood values of values at the tips assuming that the value changes by Brownian motion:: rhino2 ~/ic ยป guppy indep_c --leaf-values ic.csv ex.jplace sequence x read1 2.60377 read2 0.490566 Note that :doc:`guppy_mft` has the ``--leaf-values`` option to divide the placement weights by these inferred values. .. _(Felsenstein, 1985): http://www.jstor.org/discover/10.2307/2461605