Test case examples for bioinformatic toolkits discussed in http://biorxiv.org/content/early/2015/12/25/035360

Software used:
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
ETE3 3.0.0b35
ETE2 2.3.10
Dendropy 4.1.0
BioPython 1.63b
Newick utilities 1.6
BioPerl 1.006925
PyCogent 1.5.3

###Relevant discussion: BioPython: biopython/biopython#745

Dendropy: jeetsukumaran/DendroPy#53

BioPerl: bioperl/bioperl-live#157

newick-utilities: tjunier/newick_utils#15

Scikit-bio/PyCogent: scikit-bio/scikit-bio#1355

Original tree

((C:1.0,D:1.0)10:0.001,(A:1.0, (B:1.0,X:1.0)30:0.01)20:0.1,E:1.0)0:0.0;

Tree after rooting to X

test_ete3.py

test_ete3.py

#! /usr/bin/python

from ete3 import Tree
t = Tree('test.nw')
t.set_outgroup(t & "X")
print t.write()

Resulting newick:

(X:0.5,(B:1,(A:1,((C:1,D:1)10:0.001,E:1)20:0.1)30:0.01)1:0.5);

test_ete2.py

test_ete2.py

#! /usr/bin/python

from ete2 import Tree
t = Tree('test.nw')
t.set_outgroup(t & "X")
print t.write()

Resulting newick:

(X:0.5,(B:1,(A:1,((C:1,D:1)10:0.001,E:1)20:0.1)30:0.01)1:0.5);

test_dendropy.py

test_dendropy.py

#! /usr/bin/env python

from dendropy import Tree, TaxonNamespace

def node_label_method(tree, outgroup):
    '''Interpret node labels as node attributes (default).'''    
    outgroup_node = tree.find_node_with_taxon_label(outgroup)
    new_root = outgroup_node.parent_node
    tree.reseed_at(new_root)
    return tree

def rooted_bipartition_method(tree, outgroup):
    '''Interpret node labels as branch support values.'''

    benc = tree.encode_bipartitions()
    support_values = {}
    for nd in tree:
        support_values[nd.bipartition] = float(nd.label) if nd.label is not None else 1.0

    outgroup_node = tree.find_node_with_taxon_label(outgroup)
    new_root = outgroup_node.parent_node
    tree.reseed_at(new_root)
    tree.encode_bipartitions()
    for nd in tree:
        nd.label = support_values.get(nd.bipartition, "not_specified")
    tree.seed_node.edge.length = None
    return tree

tree = Tree.get(file=open('test.nw'), schema="newick")#, rooting="force-rooted")
rooted_bipartition_method(tree, 'X')
nw = tree.as_string(schema='newick').strip()
print nw.replace('[&R] ', '')

# Related discussion: https://github.com/jeetsukumaran/DendroPy/issues/53

Resulting newick:

(B:1.0,X:1.0,(A:1.0,((C:1.0,D:1.0)10.0:0.001,E:1.0)20.0:0.1)30.0:0.01);

test_ape.sh

test_ape.sh

#! /bin/bash
R --quiet --vanilla < test_ape.R |grep "\[1\]"|cut -f2 -d " "|cut -f2 -d '"' 

test_ape.R

library("ape")
tr <- read.tree("test.nw")
tr <- root(tr, "X")
write.tree(tr)

Resulting newick:

((((C:1,D:1)10:0.001,E:1)0:0.1,A:1)20:0.01,B:1,X:1)30;

test_patched_ape.sh

test_patched_ape.sh

#! /bin/bash
R --quiet --vanilla < test_patched_ape.R |grep "\[1\]"|cut -f2 -d " "|cut -f2 -d '"' 

test_patched_ape.R

library("ape")
source("new_root.R")
tr <- read.tree("test.nw")
tr <- root(tr, "X", edgelabel = TRUE)
write.tree(tr)

Resulting newick:

((((C:1,D:1)10:0.001,E:1)20:0.1,A:1)30:0.01,B:1,X:1);

test_newick_utilities.sh

test_newick_utilities.sh

#! /bin/bash 
./nw_reroot test.nw X

Resulting newick:

(X:0.5,(B:1.0,(A:1.0,((C:1.0,D:1.0)10:0.001,E:1.0)0:0.1)20:0.01)30:0.5);

test_biopython.py

test_biopython.py

#! /usr/bin/env python

import sys
from Bio import Phylo
trees = Phylo.parse('test.nw','newick')
t = trees.next()
t.root_with_outgroup('X')
Phylo.write(t, sys.stdout, 'newick')

Resulting newick:

(((((C:1.00000,D:1.00000)10.00:0.00100,E:1.00000)0.00:0.10000,A:1.00000)20.00:0.01000,B:1.00000)30.00:1.00000,X:0.00000):0.00000;

test_bioperl.sh

test_bioperl.sh

#!/bin/sh

# Fixes the newick output of bioperl so it can be read by ete for automatically
# generating an img
./test_bioperl.pl |sed  's/)X/,X:0)/g'|python nhx2nw.py

test_bioperl.pl

#!/usr/bin/perl
use warnings;
use strict;
use Bio::TreeIO;
use IO::String;
my $treeio = Bio::TreeIO->new(-file   => "test.nw",
                              -format => 'newick', 
                              -internal_node_id => 'bootstrap');
my $tree = $treeio->next_tree;
my $node = $tree->find_node(-id => 'X');
$tree->reroot($node);

my $out = new Bio::TreeIO(-format => 'nhx');
$out->write_tree($tree); 

Resulting newick:

((B:1,(A:1,((C:1,D:1)10:0.001,E:1)20:0.1)30:0.01)0:1,X:0);

test_pycogent.py

test_pycogent.py

#!/usr/bin/env python

from cogent import LoadTree
tr = LoadTree('test.nw')
print tr.rootedWithTip("X")

Resulting newick:

(B:1.0,X:1.0,(A:1.0,((C:1.0,D:1.0)10:0.001,E:1.0)20:0.1)30:0.01);