All the programs in this repository is for CURatio, which uses ratios of total branch lengths in gene trees to help identify phylogenetic outliers in a given set of ortholog groups from multiple genomes. An advantage of CURatio over other methods is that genes absent from and/or duplicated in some genomes can be included in the analysis. The constraint tree is the 65% consensus of presumed housekeeping genes (those with orthologues in all 12 genomes) on the JC model. For more details, please check CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths.
- Calculating the sum of branch lengths of the tree without consensus tree, b.
- Performing the neighbor-joining tree estimation of Saitou and Nei (1987).
- Computing the likelihood of a phylogenetic tree given a sequence alignment and JC model.
- Optimizing the different model parameters. We could change the shape of the phylogenentic tree.
- Calculating the sum of branch lengths of the tree with consensus tree, B.
- Inputting the consensus tree as the phylogenentic tree.
- Computing the likelihood of the phylogenetic tree given a sequence alignment and JC model.
- Optimizing the different model parameters. Do NOT change the shape of the phylogenentic tree.
-
Calculating the ratio
Ratio = B/b
- ape
- phangorn
library(ape)
library(phangorn)
phyData <- read.phyDat(file="./data/eas-ccl-wg-trimmed.fasta",format='fasta',type='DNA')
consTree <- read.tree("./consensusTree_0.65.txt")
ratio <- CURatio(phyData, consTree)
Saitou, Naruya, and Masatoshi Nei. "The neighbor-joining method: a new method for reconstructing phylogenetic trees." Molecular biology and evolution 4.4 (1987): 406-425.
For questions and concerns, please contact Qiwen Kang, qiwen.kang@uky.edu.