EvolBioInf / andi / 167

Builds Branch Commit Type Ran Committer Via Coverage
167 master improves asymmetric distance handling The anchor distance is not symmetric. i.e. d(i,j) != d(j,i). Thus we computed both distances and average the result. Now, when computing the average, the individual distances are weighted by the coverage. push kloetzl travis-ci pending completion   set done
166 master improves man page push kloetzl travis-ci pending completion   set done
165 bootstrap improves bootstrapped values The bootstrapped vales are now computed as follows: 1. Compute mean of the distance values in the two directions, weighted by coverage. 2. Apply randomness (binomial distribution). 3. Apply Jukes-Cantor correction. 4.... push kloetzl travis-ci pending completion   set done
164 master test for relative error push kloetzl travis-ci pending completion   set done
163 master count long anchors as homologous Sometimes a single long anchor spans a whole contig. Then no second anchors, neither left nor right, can be found. In this case, count the long anchor as homologous if its length is double the threshold. push kloetzl travis-ci pending completion   set done
162 manual adds comments push kloetzl travis-ci pending completion   set done
161 bootstrap Travis CI: install GSL push kloetzl travis-ci pending completion   set done
156 cutoff adds distance cutoff For closely related clades its good enough to just compare taxa within and pick one representing taxon fo comparisons with outgroups. This reduces the number of comparisons for distant genomes, and thus speeds up the computat... push kloetzl travis-ci pending completion   set done
155 cutoff fixes, wondeful fixes push kloetzl travis-ci pending completion   set done
154 cutoff adds basic estimations push kloetzl travis-ci pending completion   set done
153 v0.9.2 release v0.9.2 push kloetzl travis-ci pending completion   set done
152 master bumps version number push kloetzl travis-ci pending completion   set done
151 esa_opt <a href="https://github.com/EvolBioInf/andi/commit/0b901068e">&lt;a href=&quot;https://github.com/EvolBioInf/andi/commit/</a><a class="double-link" href="https://github.com/EvolBioInf/andi/commit/&lt;a class=&quot;do... push kloetzl travis-ci pending completion   set done
150 master adds fallback for strchrnul Apparently, `strchrnul(3)` is a GNU specific function and unavailable on BSD and Darwin (OS X). Thus we have to check for its existance and provide a fallback function. Thanks to Marc Garcia-Garcera for pointing this out. push kloetzl travis-ci pending completion   set done
149 esa_opt Merge branch 'master' into esa_opt Conflicts: src/esa.c push kloetzl travis-ci pending completion   set done