TICR: from alignments to quartet concordance factors

TICR facilitates parallel analyses of all loci, using several machines in a cluster, to handle very many genes, and many loci (very many quartets). TICR can define recombinational loci with MDL, if the alignment is very long (like one chromosome), but we do not cover this first step here. We assume that loci are already given.

General instructions are given here.

We are showing here the commands and results for the analysis of the data set in baseline.gamma0.3_n300.

Go to:

• the data
• gene trees with MrBayes
• combining gene trees samples to get concordance factors: BUCKy
• species tree from quartet CFs: Quartet MaxCut
• gene trees and species tree with RAxML & ASTRAL