bootstrapTrees - Deprecated! Please use findSwitches instead.
bootstrapTrees Phylogenetic bootstrap function.
bootstrapTrees( clones, bootstraps, nproc = 1, trait = NULL, dir = NULL, id = NULL, modelfile = NULL, build = "pratchet", exec = NULL, igphyml = NULL, fixtrees = FALSE, quiet = 0, rm_temp = TRUE, palette = NULL, resolve = 2, rep = NULL, keeptrees = TRUE, lfile = NULL, seq = NULL, downsample = FALSE, tip_switch = 20, boot_part = "locus", force_resolve = FALSE, ... )
airrCloneobjects, the output of formatClones
- number of bootstrap replicates to perform
- number of cores to parallelize computations
- trait to use for parsimony models (required if
- directory where temporary files will be placed (required
- unique identifer for this analysis (required if
- file specifying parsimony model to use
- program to use for tree building (phangorn, dnapars)
- location of desired phylogenetic executable
- location of igphyml executible if trait models desired
- keep tree topologies fixed? (bootstrapping will not be perfomed)
- amount of rubbish to print to console
- remove temporary files (default=TRUE)
- a named vector specifying colors for each state
- how should polytomies be resolved? 0=none, 1=max parsminy, 2=max ambiguity + polytomy skipping, 3=max ambiguity
- current bootstrap replicate (experimental)
- keep trees estimated from bootstrap replicates? (TRUE)
- lineage file input to igphyml if desired (experimental)
- column name containing sequence information
- downsample clones to have a maximum specified tip/switch ratio?
- maximum allowed tip/switch ratio if downsample=TRUE
- is “locus” bootstrap columns for each locus separately
- continue even if polytomy resolution fails?
- additional arguments to be passed to tree building program
A list of trees and/or switch counts for each bootstrap replicate.