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TICR: from alignments to quartet concordance factors
Claudia Solis-Lemus edited this page Aug 3, 2019
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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.
We are showing here the commands and results for the analysis of
the data set in baseline.gamma0.3_n30.
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
PhyloNetworks Workshop
- home
- example data
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TICR pipeline:
from sequences to quartet CFs
- the data
- MrBayes on all genes
- BUCKy
- Quartet MaxCut
- RAxML & ASTRAL
- PhyloNetworks: from quartet CFs or gene trees to phylogenetic networks
- TICR test: is a population tree with ILS sufficient (vs network)?
- Continuous trait evolution on a network