In makeBlastScoreTable.py added options and code for 2 additional metrics.  They can be non-symetric, so this is for the tblastn searching not the clustering.
Added option and code to retreve only a specific cluster from a specific runid in db_getPresenceAbsenceTable.py
Two scripts: downloadGenbank.py and convertGenbank2table.py to be used to download genbank files from a higher-level taxonID, collection of accesions, or existing files and convert them into the tables that we use for loading
added a rough organismTreeClusterTable.py which displaies an organismal tree, and display the genes contributing to particular clusters and proteinTreeGeneRegion.py, which displaies an protein sequence tree showing the gene region, also mark where this deviates from an organismal tree

Both need serious polishing and testing (still!)
Commit fixes to TBLastN wrapper and to orthomcl wrapper
Merge pull request #25 from JamesRH/JamesRHcommits

JamesRH commits - genbank d/l and two treeing scripts, added options for makeBlastScoreTable and db_getPresenceAbsenceTable.py
Merge branch 'master' of github.com:mattb112885/clusterDbAnalysis
Add replaceAliasesWithGeneNames.py - it is a dumb script but it works for what I used it for
Update documentation
Clean up downloadGenbank.py function - now spellchecked, cleans up temporary files automatically, output directory is a new option
Automatically generate program name in examples
Automatically generate program name in examples
Improve NCBI interface functions to produce output files with names consistent with those expected by our other scripts
Improve script compatibility with old versions of biopython (validate keyword does not exist)
Why do my readme files keep going missing??
Fixed bug in downloadGenbankFromNCBI.py - concatinate_files function call was in the wrong place
Increase return limit to avoid cutting off data from the NCBI queries for genomes within a TAXID and for genbank files within a genome
Improvements to interface with external clusters from NCBI CDD database
Added function to take an external cluster (COG, PFAM, ...) ID and obtain the RPSBLAST hits
Not all CDS entries have a translation field (believe it or not). Caught that exception and throw a warning so the whole thing doesn't die becuase of that...