tcs: Calculate TCS.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Wrapper to call t_coffee to calculate Transitive Consistency Score (TCS)

Usage

tcs(alignment, number_cores = 1, other_args = NULL, wd = here::here(), ...)

Arguments

alignment	Character vector of length one; the path to the input alignment
number_cores	Number of cores to use by t_coffee
other_args	Character vector; other arguments to pass to t_coffee. Each should be an element of the vector.
wd	Character vector of length one; the directory where the command will be run, and the external output written.
...	Additional other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

A numeric value; the overall TCS score of the input alignment.

Externally, a plain text file with TCS scores for each sequence, position, and the whole alignment. The file will be named <alignment>.score_ascii, where <alignment> is the filename of the input alignment.

Author(s)

Joel H Nitta, [e-mail]

References

Chang JM, Di Tommaso P, Notredame C. TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Mol Biol Evol. 2014 Jun. 31(6):1625-37. http://www.tcoffee.org/Projects/tcs/

Examples

## Not run: tcs("some/alignment.fasta")

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.