Release (COSPEDTree-II)

Corresponds to the version communicated to BIBM 2016

Major revision COSPEDBTree

The release contains following improvements:

1. Weighted frequency measure, computed using the coverage of taxa underlying the LCA of individual couplets
   this measure is now used as default
2. Priority measure for a couplet is updated to be the ratio of frequencies
3. We use number of queues as 1
4. NJ based method for binary refinement of the unresolved supertree now has 4 different versions:
   a) based on extra gene count between a couplet, computed for all the trees
   b) sum of branches between a couplet, computed for all the trees
   c) product of sum of branches and extra gene count
   d) product of coalescence rank and extra gene count

In addition, we mention different computation of distance matrices (for NJ based refinement) according to the
sum of values, average of values, or mode of values.

Binarized Tree

Has following extra features

1. Updated binarization with NJ and extra gene count based resolving
2. Optional dynamic score update

First release

Utilities

1. Improved version of COSPEDTree with binary supertree generation, thus named as COSPEDBTree
2. Support for both non-binary and strict binary supertree generation
3. Fastest among existing supertree approaches, with highly efficient supertree construction compared to the basic COSPEDTree approach. The performance (in terms of RF metrics) is kept identical for non-binary trees, between the earlier COSPEDTree and this package COSPEDBTree.

Limitations / Future works

1. For strict binary supertrees, as the source trees often are not complete binary, comparison leads to high number of false positive (FP) instances. We need to selectively make the tree binary (i.e. allow for some unresolved non-binary subtree in the supertree).
2. The code needs to be updated in terms of the comments, and names of few functions and variables.
3. The code needs to support Python 3.
4. The code needs to support Dendropy 4.0 (latest version).
5. The code needs to support execution on Windows XP and MacOS.