mtholder

#!/bin/sh
set -x
wget http://pypi.python.org/packages/source/D/DendroPy/DendroPy-3.11.0.tar.gz
tar xfvz DendroPy-3.11.0.tar.gz 
cd DendroPy-3.11.0
python setup.py install
cd extras/geodispersal/
python geodispersal-analysis.py LiebermanEBasidechenella.nex LiebermanEBasidechenella.nex --labels=labels.txt --paup --vicariance=vic --dispersal=disp
cat Readme.txt 

mtholder

#!/usr/bin/env python
'''Takes a MrBayes .t file and writes (to standard out) a .p file with
the parameters being the edge lengths for each of the Terminal edges.

This .p file can be used with Tracer http://tree.bio.ed.ac.uk/software/tracer/
or other MCMC diagnostics files.

Example invocation with redirection to a file called term_edges_myrun.p :

    python terminal_edges_to_dot_p.py myrun.t > term_edges_myrun.p

mtholder

import sys
import dendropy
from copy import copy
threshold = float(sys.argv[1])
filename_list = sys.argv[2:]
SCRIPT_NAME = 'conflict_viz'

def debug(*valist):
    msg = ' '.join([str(i) for i in valist])
    sys.stderr.write(SCRIPT_NAME + ': ' + msg + '\n')

mtholder

#!/usr/bin/env python
import sys
import dendropy

if __name__ == '__main__':
    from optparse import OptionParser
    from optparse import OptionGroup
    import sys, os
    
    _script_name = os.path.split(sys.argv[0])[1]

mtholder

#!/usr/bin/env python
def balanced_tree(n, level):
    if level == 0:
        return n + 1, 't%d' % n
    n, leftsub = balanced_tree(n, level - 1)
    n, rightsub = balanced_tree(n, level - 1)
    return n, '(%s,%s)' % (leftsub, rightsub)

if __name__ == '__main__':
    import sys