Species tree from quartet CFs: QMC

Quartet MaxCut (QMC) uses quartets as input, and returns a tree containing as many input quartets as possible. The goal is similar to the goal of ASTRAL, but the input is different: quartets instead of gene trees. We will use this QMC tree as a starting tree to search for a better tree (or network) under a likelihood-based criterion.

To extract quartets with highest CFs and use them as input to QMC to get a tree, we can use the get-pop-tree.pl script:

$ ../scripts/get-pop-tree.pl bucky-output/1_seqgen.CFs.csv

Script was called as follows:
perl get-pop-tree.pl bucky-output/1_seqgen.CFs.csv

Parsing major resolution of each 4-taxon set... done.
Running Quartet Max Cut...

Quartet MaxCut version 2.10 by Sagi Snir, University of Haifa
quartet file is 1_seqgen.QMC.txt,
Number of quartets is 15, max element 6
Number of quartets read: 15, max ele 6
Started working at  Mon May 23 09:44:12 2016
Ended working at  Mon May 23 09:44:12 2016

Quartet Max Cut complete, tree located in '1_seqgen.QMC.tre'.

We have a new file 1_seqgen.QMC.tre with our QMC tree. And can look at it, then organize results. A good place this tree in the bucky folder:

$ cat 1_seqgen.QMC.tre
$ mv 1_seqgen.QMC.tre bucky-output
$ ls bucky-output/
1_seqgen.BUCKy.tar 1_seqgen.CFs.csv 1_seqgen.QMC.tre 1_seqgen.mb.tar 1_seqgen.mbsum.tar.gz

Next: an alternative pipeline to get gene trees and species tree with RAxML & ASTRAL.