Releases: lonelyjoeparker/qmul-genome-convergence-pipeline
CONTEXT Phylogenomics dataset browser - v0.8.4 prerelease
CONTEXT is a browser for phylogenomic datasets (alignments and trees).
See the README for more information.
It's a standalone Java application which tries to make it easy to sort, view, and compare large numbers of alignments or phylogenies. Various descriptive statistics (alignment/tree dimensions; signal content; gap proportions; invariant sites etc) and their summary statistics are calculated and can be exported.
You should be able to run CONTEXT with this command:
java -jar CONTEXT-v0.8.4prerelease.jar
It is however recommended that additional memory (at least 2Gb) is allocated for very large datasets - more than around 3000 alignments * tens of taxa * thousands of bp, for instance. Use the -XmxMg -XmsSg switches for this, where M is the number of Gb extra RAM:
java -XmxMg -XmsSg -jar CONTEXT-v0.8.4prerelease.jar
Use it to screen your alignments and/or trees prior to downstream analyses, e.g. to detect outliers before you analyse them. You can also plot univariate and bivariate distributions for alignment statistics, to explore correlations in the data.
Roadmap
This is intended to be the final version of CONTEXT before the full, public (publication) release, v0.9.0.
We'll start work on changes (based on user feedback) for 0.9.1+ after six months, aiming for a 1.0 release a year from now.
Changelog v0.8.4
UI improvements:
- Charts and summary statistics for alignment stats
- Scrolling behaviour improved for alignments
- Tree statistics reported
- (Limited) support for phylogenies as NEXUS in addition to existing PAML/Phylip/strict NEWICK.
Method improvements:
- Tree statistics implemented
- Full translation of all possible codons, not just common ones
Robustness improvements:
- Error reporting improved
- Command-line output less verbose
- File I/O debugged somewhat