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#!/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

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#!/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]

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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
'''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

#!/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 

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#!/usr/bin/env python
import sys, math
v_list = [float(value) for value in sys.stdin]
offset = max(v_list)
n = len(v_list)
sum_exps = sum([math.exp(v - offset) for v in v_list])
mean_exps = sum_exps/n
sys.stdout.write('Log of mean of the exp of %d values is:\n' %  n)
sys.stdout.write('%8.7f\n' % (math.log(mean_exps) + offset))

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#!/bin/sh
# You might want to modify the first line to specify your own install location.
#    In theory the rest should not need tweaking...
export GCC_PREFIX="$HOME/gcc4.7"

# Hopefully, you can tweak these as they get out of date, but the download URL's
#      may not be stable to text substitution.
GMP_DOWNLOAD_VERSION=gmp-5.0.5
MPFR_DOWNLOAD_VERSION=mpfr-3.1.0
MPC_DOWNLOAD_VERSION=mpc-0.8.2

mtholder

#!/usr/bin/env python
'''
Example of a client of the demo of the TNRS API described at:
    http://www.evoio.org/wiki/Phylotastic/TNRS

Reads names (separated by newline characters) from file names passed in as
    command-line arguments (or reads name from standard input if no arguments
    are given).

Outputs tab-delimited summary of the matches for each query sorted by score of 

mtholder

#!/bin/sh
# Script to use NCLconverter to convert TreeBase NEXUS files to newick
# Invocation:
#   sh range_of_treebase2newick.sh 10000 10100
# in a directory with filenames like S10001.nex to convert each file
# name like S10000.nex up to file S10100.nex to newick.
# you should get files like:
#   outS####.tre  newick tree for the first trees block
#   2outS####.tre , 3outS####.tre , etc if the file has multiple output blocks
#   outS####.NameTranslationFile.txt is an ad hoc xml description of the name mapping

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//	Copyright (C) 2012 Mark T. Holder
//
//	Based on example/splitsinfile/splitsinfile.cpp in NEXUS class library
//
//	After NCL has been installed at ${NCL_PREFIX}
//
//		g++ newick2taxalist.cpp -o newick2taxalist -I "${NCL_PREFIX}/include" -lncl -L "${NCL_PREFIX}/lib/ncl"
//
//	Takes a newick file and prints out the taxa labels, one per line.
//