CHANGES IN VERSION 1.12.0 ------------------------ NEW FEATURES o Add function orgKEGGIds2EntrezIDs to fetch the mapping between KEGG IDs and Entrez IDs o Add function makeAxtTracks o Add function addAncestorGO CHANGES IN VERSION 1.10.0 ------------------------ NEW FEATURES o Updated CNE class for storing all the information about running the pipeline. o Add read.rmMask.GRanges to read RepeatMasker .out file. o Add read.rmskFasta to read soft repeat masked fasta file. o Add the distribution plot of axt alignment matches. o Add the distribution plot of CNE length. o Add the syntenicDotplot for axt alignment and GRangePairs. o When readAxt and readBed, seqinfo is kept when available. o New fixCoordinates function makes the coordinates of Axt alignments always relative to positive strands. o Add parallel subAxt for Axt alignment. o Add the plot of genomic distribution of CNE. o Add the function to make bed and bigwig files of CNEs. BUG FIXES o Instead of an error, an empty GRangePairs is returned when no CNEs identified. CHANGES IN VERSION 1.8.0 ------------------------ BUG FIXES o Fix a bug caused by "format" in the blat step. NEW FEATURES o Add the pairwise whole genome alignment pipeline o Add a new class "GRangePairs" o "Axt" class is now based on "GRangePairs" class. o readAncora for reading Ancora format CNE files.