quartetCF: Quartet concordance factors across Arabidopsis thaliana
In phylolm: Phylogenetic Linear Regression
Description
Usage
Format
References
Description
Concordance factors of quartets for 29 A. thaliana accessions and A. lyrata,
obtained from chromosome 4 using MDL to delimit loci
then
BUCKy on each 4-taxon set.
Usage
1
Format
Data frame with 7 variables and 27,405 rows.
Each row corresponds to one 4-taxon set
(choosing 4 taxa out of 30 makes 27,405 combinations).
The first four variables, named 'taxon1' through 'taxon4',
give the names of the 4 taxa in each 4-taxon set.
Variables 5 through 7 are named CF12.34, CF13.24 and CF14.23,
and give the estimated concordance factors of the 3 quartets on
each set of 4 taxa: taxon 1 + taxon 2 versus taxon3 + taxon 4, etc.
These concordance factors are the proportion of loci that have a
given quartet tree.
They were obtained from chromosome 4 using MDL to delimit loci
then BUCKy to estimate quartet concordance factors (CFs).
References
Stenz, Noah W. M., Bret Larget, David A. Baum and Cécile Ané (2015).
Exploring tree-like and non-tree-like patterns using genome sequences:
An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh.
Systematic Biology, 64(5):809-823.
TICR pipeline: github.com/nstenz/TICR
phylolm documentation built on July 2, 2020, 3:44 a.m.
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Description Usage Format References
Description
Concordance factors of quartets for 29 A. thaliana accessions and A. lyrata, obtained from chromosome 4 using MDL to delimit loci then BUCKy on each 4-taxon set.
Usage
1 |
Format
Data frame with 7 variables and 27,405 rows. Each row corresponds to one 4-taxon set (choosing 4 taxa out of 30 makes 27,405 combinations). The first four variables, named 'taxon1' through 'taxon4', give the names of the 4 taxa in each 4-taxon set. Variables 5 through 7 are named CF12.34, CF13.24 and CF14.23, and give the estimated concordance factors of the 3 quartets on each set of 4 taxa: taxon 1 + taxon 2 versus taxon3 + taxon 4, etc. These concordance factors are the proportion of loci that have a given quartet tree. They were obtained from chromosome 4 using MDL to delimit loci then BUCKy to estimate quartet concordance factors (CFs).
References
Stenz, Noah W. M., Bret Larget, David A. Baum and Cécile Ané (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology, 64(5):809-823.
TICR pipeline: github.com/nstenz/TICR
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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