<commit_before>PhyloBlend
==========

###<strong>Description:</strong>

Python pipeline to pull out sequence sets for the cluster-based mid-point rooted tree set released from the Phylota database. It will also allow expansion of the sequence set with BLAST searches, followed up with a new sets of alignments and tree construction. Other features are in there, but not described here yet.

<i>Instructions below are for a [Debian](www.debian.org) based OS like [Ubuntu](www.ubuntu.com)</i>

###<strong>Requirements (Quick List):</strong>


1. [Python 2.7](www.python.org)</li>
2. [Numpy](www.numpy.org)</li> <pre>sudo apt-get install python-numpy</pre>
3. [Sci-py](www.scipy.org)</li> <pre>sudo apt-get install python-scipy</pre>
4. [Biopython](www.biopython.org/wiki/Main_Page)</li> <pre>sudo apt-get install python-biopython</pre>
5. [Graph-tool](www.graph-tool.skewed.de/)</li>
6. [IVY](www.reelab.net/home/software/ivy/)</li>
7. [Muscle]() for Alignments <pre>sudo apt-get install muscle</pre>
8. [RAxML]() for Tree Building <pre> sudo apt-get install raxml</pre>
9. Local copy of [Phylota]( (www.phylota.net/pb/Download/) mySQL database</li>
10.Local copy of [NCBI BLAST](www.blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)<pre>sudo apt-get install ncbi-blast+</pre>  
11.[*nt*](ftp.ncbi.nlm.nih.gov/blast/db) database

###**Detailed Setup:**

Coming soon.<commit_msg>Beautify<commit_after>PhyloBlend
==========

###<strong>Description:</strong>

Python pipeline to pull out sequence sets for the cluster-based mid-point rooted tree set released from the Phylota database. It will also allow expansion of the sequence set with BLAST searches, followed up with a new sets of alignments and tree construction. Other features are in there, but not described here yet.

<i>Instructions below are for a [Debian](www.debian.org) based OS like [Ubuntu](www.ubuntu.com)</i>

###<strong>Requirements (Quick List):</strong>


1. [Python 2.7](www.python.org)</li>
2. [Numpy](www.numpy.org)</li> <pre>sudo apt-get install python-numpy</pre>
3. [Sci-py](www.scipy.org)</li> <pre>sudo apt-get install python-scipy</pre>
4. [Biopython](www.biopython.org/wiki/Main_Page)</li> <pre>sudo apt-get install python-biopython</pre>
5. [Graph-tool](www.graph-tool.skewed.de/)</li>
6. [IVY](www.reelab.net/home/software/ivy/)</li>
7. [Muscle]() for Alignments <pre>sudo apt-get install muscle</pre>
8. [RAxML]() for Tree Building <pre> sudo apt-get install raxml</pre>
9. Local copy of [Phylota]( (www.phylota.net/pb/Download/) mySQL database</li>
10. Local copy of [NCBI BLAST](www.blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)<pre>sudo apt-get install ncbi-blast+</pre>  
11. Local copy of the NCBI [*nt*](ftp.ncbi.nlm.nih.gov/blast/db) database

###**Detailed Setup:**

Coming soon.
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