IgPhyML: Function that calls IgPhyML to calculate a phylogenetic tree...

In Fraternalilab/BrepPhylo: BrepPhylo: R package for phylogenetic analysis of B cell repertoire

Function that calls IgPhyML to calculate a phylogenetic tree and returns it including meta-data.

Description

Note, that what this function implements is a two-step optimization: First, the topology is searched for using M0/GY49 (Goldman and Yang (1994); Yang and Bielawski (2000)), then this topology is fixed and used as starting point for the fitting by the HLP17 model (specialized for antibody lineages Hoehn, Lunter and Pybus (2017)). One could further optimize the topology by specifying "-o tlr" instead of "-o lr".

Usage

IgPhyML(
  path,
  root,
  accuracy = "basic",
  executable = "",
  log = NULL,
  useTempDir = TRUE
)

Arguments

path	Input FASTA file path.
root	Root ID (germline sequence).
accuracy	Either "basic", "high" or "extreme", this parameter affects the internal calls of IgPhyML which will affect runtime considerably (default: "basic").
executable	If not empty, this file will be used for the call of IgPhyML otherwise the function will attempt to find the executable (default: "").
log	If not NULL, log entries over the execution will be written to the given connection.
useTempDir	If TRUE, generate temporary directory and write results there. (default: TRUE)

Value

A list holding the intermediary and final trees and additional data (elements: "success", "topology", "fit" )/

Examples

## Not run: IgPhyML( path = "/path/to/input.fasta", root = "V4-59" )

Fraternalilab/BrepPhylo documentation built on Jan. 3, 2025, 10:03 a.m.