Xenogi

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- Separated functions doing alignments and tree making for the sake of compatibility with PHANTASM.

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- Now have the option to use GeneRax to create gene trees in a species-tree aware way. If useGeneRaxToMakeSpeciesTrees is set to True (as is the case in the default params.py) GeneRax will be used. If False, FastTree is used. GeneRax makes the gene trees more accurate, and cuts down on spurious events in our reconciliations. However there is a significant cost in terms of speed (about 2 fold on our example data set).
- Now using MUSCLE v5
- Added an aminoAcidIdentity flag which uses blast output to calculate the average amino acid identity between strains.

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This is a major release, meaning things like parameter files and output files have changed.

- Now reconstruct the history of gene families by reconciling the gene tree for a family against the species tree. We use FastTree to make the gene trees, and a custom reconciliation algorithm called DTLOR (duplication, transfer, loss, origin, rearrangement) to do the reconciliation. The analysis output now includes a history of evolutionary events for each gene, as well as an explicit call as to its origin (either core gene, C, or xeno hgt event, X).
- Added a refine step which comes after makeIslands. This step focuses on cases where there are multiple most parsimonious reconciliations, and chooses the one most consistent with nearby families.
- Added rooted and unrooted tree classes to make working with gene trees more convenient.
- printAnalysis now produces a tab delimited (islands.tsv) file in addition to the more human readable islandsSummary.txt.
- Added some additional fields to blast output files.
- xenoGI gene names now encorporate locus tag rather than protein ID.
- Added a tutorial (TUTORIAL.rst) to the repository.

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- runBlast now checks to see if a particular comparison has already been run, and if so doesn't repeat. This is mostly needed for a development version working with large numbers of species.
- Replaced the geneNames object with a genes object more suitable to large numbers of strains (thousands).
- The string form of gene names now also contains the number.
- Now use string based names for nodes only, rather than numerical and string. As a part of these changes, we've created a strainInfo file, and a corresponding parameter strainInfoFN in the example params.py.
- parseGenbank can now optionlly create dna files (depending on the new parameter dnaBasedGeneTrees).
- added makeSpeciesTree option. This makes gene trees for the hard core set of gene families (using FastTree with GTR+CAT) and then combines them into a species tree using ASTRAL.
- Updated example assemblies so they mostly are from type strains.
- Changed the parameter numThreads to be called numProcesses (since that's a more acurate description of what's being done under the hood).

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- Fixed a bug in island formation that arose when there were no islands on a branch.
- Changed naming for blast files to avoid conflicts with strain names. (In particular with the '-' character.)
- parseGenbank now throws an error when it encounters a gbff file that lacks protein annotations.
- Created a sharedScores class that shares memory between separate processes. This reduces memory usage significantly in calcScores.

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This is a major release, meaning things like parameter files and output files have changed.

- Reduced RAM requirements. We've eliminated the norm score. Synteny scores are now based on raw scores, and thresholds for family formation calculated directly for each strain pair.
- Improved speed. This results from changes to island formation, and makes a particularly big difference for large data sets (50 or more strains).
- Simplified the user parameters file. Parameters users are unlikely to ever change have been moved elsewhere.
- Added plotScoreHists flag. Makes rawSc.pdf, synSc.pdf, coreSynSc.pdf.
- Introduced several additional classes (LocusFamily, LocusIsland). This is largely for the sake of future development, and should make it easier to capture things like gene duplication.
- Modified Score class to better organize scores from particular strain pairs. This means the current version of xenoGI will not read scores objects from older versions.

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