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treeCl 0.0.5

Phylogenetic Clustering Package

# ``treeCl`` - Phylogenetic Tree Clustering

``treeCl`` is a python package for clustering gene families by
phylogenetic similarity. It takes a collection of alignments, infers their phylogenetic trees,
and clusters them based on a matrix of between-tree distances. Finally, it calculates a single representative tree for each cluster.

The purpose of this is to establish whether there is any underlying structure
to the data.

## Installation

####Make sure you have the dependencies required for installation - numpy, and cython (```pip install cython numpy``` if you don't)

###The ```setup.py``` way:

1. Pick a nice directory to put the files in. It can be anywhere, you won't need them again once they are installed. We'll call this ```$TEDIOUS_BUILDING_AREA```

2. Clone the repo:

``` bash
cd $TEDIOUS_BUILDING_AREA
git clone https://github.com/kgori/treeCl.git tiresome_software
cd tiresome_software
python setup.py install
```

###The pip way:

```pip install git+https://github.com/kgori/treeCl.git```

## Dependencies

#### Python:
- [matplotlib]http://matplotlib.org/ "matplotlib")
- [numpy]http://www.numpy.org "NumPy") (v1.6.2)
- [scipy]http://www.scipy.org "SciPy") (v0.11.0)
- [dendropy]http://pythonhosted.org/DendroPy/ "DendroPy is a Python library for phylogenetic computing.") (v3.12.0)
- [scikit-learn]http://scikit-learn.org/stable/ "Machine learning in Python") (v0.12.1)
- [biopython]http://www.biopython.org/‎ "Biopython") (v1.60) *optional - for k-medoids clustering only*

The install process should take care of installing these for you, except numpy and cython (see Installation section, above).

#### External:
treeCl uses some external software, namely ALF for simulating sequences, and PhyML for calculating trees and likelihoods.
- [ALF]http://darwin-services.inf.ethz.ch/DarwinServices/ALF.html#service0 "ALF: simulating genome evolution")
- [PhyML]https://code.google.com/p/phyml/ "Phylogenetic estimation using Maximum Likelihood")
- [Darwin]http://www.cbrg.ethz.ch/darwin "Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences")

#### Bundled:
- [GTP]http://dl.acm.org/citation.cfm?id=1916603 "ACM digital library") - a java program for calculating geodesic distances - see [A Fast Algorithm for Computing Geodesic Distances in Tree Space]https://cs.uwaterloo.ca/~m2owen/pub/poly_geodesic.pdf "Owen and Provan, 2011")

## Example Analysis
``` python
"""
Import some classes from treeCl
"""
from treeCl import Collection, Scorer, Clustering, Partition, DistanceMatrix


"""
Load your data. This should be a directory full of sequence alignments in fasta '*.fas'
or phylip '*.phy' formats.
"""
c = Collection(input_dir='input_dir', file_format='phylip',
datatype='protein') # add compression='gz' or 'bz2'
# if sequence alignments are compressed
# (zip not supported yet)

"""
Calculate some trees. Trees can be Neighbour Joining ('nj') or maximum
likelihood ('ml'), or an intermediate algorithm where the topology is
done by NJ, and the branch lengths are done by ML.
The intermediate algorithm is run with
c.calc_NJ_trees(analysis='lr') # 'lr' = 'lengths and rates'
"""
c.calc_NJ_trees() # add verbosity=1 or higher to get progress messages
# c.calc_ML_trees() # use maximum likelihood - slower, more accurate

"""
Now get the distance matrix of between-tree distances and set up a clustering object
"""
dm = c.distance_matrix('euc')
cl = Clustering(dm)


"""
Do some clustering. Syntax is
cl.hierarchical(<number_of_clusters:int>, <method:str>)
'method' is one of 'single', 'complete', 'average', 'ward'
cl.kmedoids(<number_of_clusters:int>)
cl.spectral_cluster(<number_of_clusters:int>, <decomp:decomp>)
cl.MDS_cluster(<number_of_clusters:int>, <decomp:decomp>)

Spectral and MDS methods need a 'Decomp' object, which is an eigen decomposition
into eigenvalues and eigenvectors. These are obtained with:
decomp = cl.spectral_decomp(-1, 'median') # The -1 and 'median' parameters seem to work best
decomp = cl.MDS_decomp()
"""

p = cl.hierarchical(2, 'single') # example single-linkage hierarchical
# clustering into 2 groups

"""
Score the result via likelihood
"""
sc = Scorer(c.records, analysis='nj') # or 'ml' or 'lr'
score = sc.score(p)
print score

"""
Finally, get the sequences and trees for the two groups
"""

groups = p.get_membership()
sequences1 = sc.concatenate(groups[0]) # sequences1.write_fasta('filename')
# or .write_phylip('filename',
# interleaved=True)
sequences2 = sc.concatenate(groups[1])

tree1 = sc.concats[groups[0]]
tree2 = sc.concats[groups[1]]

```
 
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