josephwb

#!/bin/bash

# report files greater than some size (default 100 MB)
# does so recursively starting at some dir (default pwd)

# to make executable, do:
# chmod +x find_large_files.sh

print_help () {
    echo "Recursively find all files larger than some size"

josephwb

require(phangorn);

# check the monophyletic status of every genus in the tree `phy`
check_genus_monophyly <- function (phy) {
    # get genera. assumes form: Genus_species_whatever
    gens <- sort(unique(sub("_.*", "", phy$tip.label)));
    n <- length(gens);
    cat("Checking ", n, " genera for monophyly status.\n", sep="");
    # the number of descendant tips of the MRCA. preallocate for monotypic genera
    ndec <- rep(1, n);

josephwb

library(ape);

# like keep.tip, but you can keep internal nodes toooooo
keep.nodes <- function (phy, nds) {
  # stats
  Ntip <- length(phy$tip.label);
  NEWROOT <- Ntip + 1;
  Nnode <- phy$Nnode;
  hasNL <- !is.null(phy$node.label);