* Bumped standard to 3.9.1, no changes required. * New upstream version. - major additions to Cookbook - added AlleleFreqs attribute to ensembl Variation objects. - added getGeneByStableId method to genome objects. - added Introns attribute to Transcript objects and an Intron class. - added Mann-Whitney test and a Monte-Carlo version - exploratory and confirmatory period estimation techniques (suitable for symbolic and continuous data) - Information theoretic measures (AIC and BIC) added - drawing of trees with collapsed nodes - progress display indicator support for terminal and GUI apps - added parser for illumina HiSeq2000 and GAiix sequence files as cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser. - added parser to FASTQ files, one of the output options for illumina's workflow, also added cookbook demo. - added functionality for parsing of SFF files without the Roche tools in cogent.parse.binary_sff - thousand fold performance improvement to nmds - >10-fold performance improvements to some Table operations