--- Release notes MEGAN /V5_11_3: --- - Fixed bug in BIOM1 output - Added “report only official ranks” option to BIOM1 output - Minor bug fixes GUI --- Release notes MEGAN /V5_11_2: --- - Modified multilevel STAMP export such that missing taxon rank labels are replaced by labels in brackets --- Release notes MEGAN /V5_11_1: --- - Added multi-level taxonomic export to STAMP --- Release notes MEGAN /V5_11_0: --- - Added new “Export to STAMP” command - Export to BIOM still problematic, please use MEGAN6 if you need this feature --- Release notes MEGAN /V5_10_7: --- - Fixed bug in CSV exporter that prevented export of read name to seed-path and similar - Fixed BIOM-related bug that prevented use of some BIOM menu items --- Release notes MEGAN /V5_10_6: --- - Fixed serious (recently introduced?) bug that prevented use of GI mapping file --- Release notes MEGAN /V5_10_5: --- - fixed bug in commandline version of "extract to new document" command --- Release notes MEGAN /V5_10_4: --- - a number of minor bug fixes --- Release notes MEGAN /V5_10_3: --- - fixed (recently introduced bug) that prevented use of rarefaction tool --- Release notes MEGAN /V5_10_2: --- - fixed bug that caused all reads parsed from a SAM file to be given the same name in the case that no fastA file was given --- Release notes MEGAN /V5_10_1: --- - Added Reset Window location to Window menu to address problem that windows sometime disappear offscreen… - Fixed bug in Taxonomy name parser for BLASTN files --- Release notes MEGAN /V5_10_0: --- - New release of GI to taxonomy mapping file fixes problem of low assignment of reads to taxa - Separate files for protein and nucleotide mapping files have been replaced by a single mapping file - Update to latest version of NCBI taxonomy (as of March 2015) - Better heuristic for guessing name of FASTA or FASTQ file for given BLAST file - Consolidated charts code - fixed bug that suppressed No Hits, Unassigned and Low Complexity nodes in KEGG viewer - added support for read magnitudes when parsing SAM format - fixed bug that caused MEGAN to report double the amount of reads parsed when parsing BlastTab format - fixed bug that caused MEGAN to display length rather than weight as weight of read in Inspector window - now use compression in RMA3 files - KEGG mapping now uses indexed binary format. Extended KEGG mapping by considering as all GI numbers that occur on the same header line in the NR database as equivalent - MALT SAM format updated to be compatible with sam-tools and picard-tools - SAM parser updated to handle modified SAM format generated by MALT 0.1.0 - fixed BlastParser so now DIAMOND SAM files are parsed into RMA3 format - fixed bug in blast2lca that caused program to terminate on some input files --- Release notes MEGAN /V5_9_1: --- - Fixed bug introduced in V5.9.0 that prevented sam2rma from running - Implemented memory-mapped access to gi-to-taxid bin file for speedup of mapping process - Fixed bug that cased tree and network cluster viewer to draw nodes as tiny circles --- Release notes MEGAN /V5_9_0: --- - fixed a number of bugs that prevented alignment and reanalysis of DNA sequences when no taxon assignment computed - added caching to GI lookup to speedup parsing when using GI lookup file - implemented PFAM analyzer for testing, not generally available yet - implemented Voronoi tree map for testing, not generally available yet - updated NCBI tree - updated GI-to-taxon mapping files available for download --- Release notes MEGAN /V5_8_6: --- - fixed a number of bugs related to selection in chart viewers - added new tool blast2lca that can be used as a stand-alone LCA mapper - some modifications to the Open From Server dialog --- Release notes MEGAN /V5_8_5: --- - Fixed bug in Chart viewer that prevented the selection of taxa or other items by clicking on their labels - Fixed bug that prevented access to “Open From Server…” menu item when in Chart viewer - Fixed bug that made it impossible to inspect reads and alignments of remote files --- Release notes MEGAN /V5_8_4: --- - Modified tools/sam2rma so that it uses bundled JRE on MacOS and uses MEGAN memory settings. This fixes the problem that sam2rma didn’t work on MacOS installations running Java 6. - Fixed Mnemonics assignment for windows and linux (some menu items were given the same mnemonic) --- Release notes MEGAN /V5_8_3: --- - added “set max radius” menu item for co-occurrence network plot - updated manual - added new tools directory (linux and MacOS versions) - added SAM2RMA program to tools directory, a standalone Java program that can be used to produce a MEGAN RMA file from a SAM file (or files) generated by DIAMOND or MALT - minor bug fixes - (second attempt) --- Release notes MEGAN /V5_8_2: --- - Added button to report info about MeganServer instance - Fixed bug in progress bar when load data from MeganServer - Update in both MEGAN and MeganServer,, require newest version of MEGAN to use MeganServer --- Release notes MEGAN /V5_8_1: --- - Fixed bug that caused installer not to remove old files, thus leading to unreproducible errors... --- Release notes MEGAN /V5_8_0: --- - Added field for short description of sample to Import Blast dialog - Added Open From Server… menu item - Setup default server megan-db.org/Permafrost - Updated manual - Updated bundled java versions (windows and mac) --- Release notes MEGAN /V5_7_2: --- - modified import blast dialog so that new name is suggested for rma file if an rma already exists - megan server browser works, use the following command to enable it (for testing only): setprop allow-meganserver=true - a couple of bug fixes --- Release notes MEGAN /V5_7_1: --- - Fixed bug in installer that caused set memory allowance to be ignored under MacOS. This bug caused MEGAN to run extremely slowly because the program was only given 900M of memory. - Fixed bug that caused graphics to be incomplete when produced using command line mode. In fact this fixes a major issue with the command line version that caused multiple problems. --- Release notes MEGAN /V5_7_0: --- - Updated taxonomy to Nov 15, 2014 - Updated gi-to-taxon mapping files available from MEGAN website - Fixed bug in comparison. Now, when using normalization or subsampling in comparison together with “Ignore all unassigned reads”, the new sample size equals the smallest number of assigned reads in any of the input files (and not the smallest total number of reads) - Fixed minor bug that prevented correct display of minSupportPercent in some cases - Fixed bug that caused error in query coordinates when parsing hard masked SAM matches - Fixed bug that caused completely incorrect alignments when parsing soft masked SAM matches - Fixed minor bug in SAM format associated with inserts in MD string that are followed by ‘0 --- Release notes MEGAN /V5_6_6: --- - Fixed bug in Taxonomy Chart viewer that prevented from web search from working - Failed to fix bug in Word cloud viewer that causes selection not to work correctly --- Release notes MEGAN /V5_6_5: --- - Fixed bug that prevented some selection commands from working --- Release notes MEGAN /V5_6_4: --- - fixed bug in Extract reads dialog that threw null-pointer exception when node has no assigned reads - On MacOS, file open dialogs now allow selection of multiple files - In Blast Import dialog, multiple BLAST or FastA files are now specified in file open dialog and no longer by a subsequent dialog --- Release notes MEGAN /V5_6_3: --- - MEGAN5 now requires Java 1.7, won’t run with 1.6 - Bundled latest version of Java 1.7 with Windows and Mac installers - MEGAN now requires MacOS 10.7 - Updated to latest version of NCBI taxonomy - Modified license file parser to accept files in RTF format - Fixed a number of minor bugs --- Release notes MEGAN /V5_6_3: --- - MEGAN5 now requires Java 1.7, won’t run with 1.6 - Bundled latest version of Java 1.7 with Windows and Mac installers - MEGAN now requires MacOS 10.7 - Updated to latest version of NCBI taxonomy - Modified license file parser to accept files in RTF format - Fixed a number of minor bugs --- Release notes MEGAN /V5_6_2: --- - fixed some minor issues with the alignment viewer --- Release notes MEGAN /V5_6_1: --- - Added alignment-assisted assembly of all reads aligned to a particular reference sequence. Resulting contigs can be saved in fastA format - Added assembly-based sorting of reads in alignment viewer --- Release notes MEGAN /V5_6_0: --- - Implemented three-dimensional PCoA plots - Fixed a number of bugs in PCoA viewer --- Release notes MEGAN /V5_5_4: --- - fixed bug in “Compute Taxonomic Profile” dialog that prevented use of this feature - fixed a number of minor bugs associated with opening and positioning new windows - fixed bug associated with turning bi-vectors on and off - fixed a couple of other minor bugs - went back down to java 1.6 (from 1.7) --- Release notes MEGAN /V5_5_3: --- - Fixed bug that prevented MEGAN from opening windows in web browsers under Windows --- Release notes MEGAN /V5_5_2: --- - Added calculation and display of BiPlot vectors to PCoA plot (new menu items Show BiPlot and BiPlot Size) - Fixed newly introduced bug in scale-bars associated with PCoA plot --- Release notes MEGAN /V5_5_1: --- - Modified ClusterViewer so that ecological indices are only calculated from explicitly selected nodes (in the past, if no nodes were selected in the main view, then all leaves were used) - Fixed major bug that caused CogClusterViewer to use counts from MainViewer, not from the CogViewer - Reorganised tool bars slightly --- Release notes MEGAN /V5_5_0: --- - Implemented square root of Jensen-Shannon divergence (see Arumugam et al. 2011) as new ecological index calculation (new beta diversity measure) - Removed UniFrac calculation from menus (while this is the UniFrac algorithm, UniFrac is usually not applied to a binning but rather to a phylogenetic tree, so this was a potential source of confusion) - Added new lcaPercent parameter that instructs MEGAN to place read above given percent of matched taxa. - Fixed bug in Blast Parser that assigned incorrect expected value when BLAST text contained “Expected(2) = …” rather than “Expected = …” Parser now ignores everything between “Expected” and “=“ - Added new “Join Nodes” command in PCoA plot and Sample viewer. Selected nodes, or nodes representing samples that have the same value of some given attribute are visually “joined” using in the PCoA viewer using their convex hull - Modified “Check for Updates” command so that an available update is opened from within MEGAN --- Release notes MEGAN /V5_4_3: --- - Fixed bug in Find tool bar (multiple occurrences of “From File” check box) - Added command line execute to MacOS and Linux installation, these do not require -g option and these do not invoke the autoupdater - Providing more than one command to -x option now throws fatal exception - Fixed missing references in manual --- Release notes MEGAN /V5_4_2: --- - Fixed bug that effected Collapse to Kingdom and similar commands, causing too many nodes to be displayed - Modified taxon-to-counts DSV exporter so as to list nodes that have 0 counts as well. - Changed layout of toolbar to always display all buttons - Added Rank… button to toolbar - Added “uncollapse” button to taxon find dialog that makes MEGAN search among currently collapsed nodes as well - Added message indicating current taxonomic rank displayed - Put more up-to-date gi-2-taxon-id mapping on website --- Release notes MEGAN /V5_4_1: --- - Upgraded to Java 7 - Bundled JRE with Apple and Window installers - Fixed recent bug that prevented use of SEED classification --- Release notes MEGAN /V5_4_0: --- - Updated SEED classification to release release 59 (2012) - Fixed bug that prevented use of “set context” command - Modified “set context” command so that “set context=?” lists all currently available contexts - Fixed newly introduced bug that caused error when using the “Load all reads into memory” import option - Modified RAPSearch2 .aln parser to accommodate recent change of format produced by RAPSearch2 - Fixed bug that prevented canceling “Save As…” under Windows. - Added new minSupportPercent feature that sets the min support value as a percentage of the total reads assigned --- Release notes MEGAN /V5_3_0: --- - Fixed bug in Collapse Genus etc - caused tree to uncollapse to wrong nodes - Fixed bug in Extract Reads dialog that caused single file to be overwritten when saving data from multiple nodes - Fixed bug in “show match” command in alignment viewer - Fixed bug that prevented MEGAN from opening windows in a browser when using Java 7 on MacOS X - Fixed bug in RAPSearch2 parsing code that caused COG assignments to be ignored - Fixed bug in LCA algorithm (only occurs when all matches for a read are to the same taxon) - Added support for experimental RMA3 format (internal use only until fully debugged) --- Release notes MEGAN /V5_2_3: --- - Fixed bug that caused chart viewer to generate many expections when mouse moved over chart - Fixed bug in chart viewer that prevented tooltips from appearing over parts of chart --- Release notes MEGAN /V5_2_2: --- - Fixed major bug in DSV taxonomy profile parser - Fixed bug that prevented selection in charts - Partially fixed bug that buries modal dialogs under other megan windows --- Release notes MEGAN /V5_2_1: --- - Fixed bug that prevented version 5.2.0 from running under linux or windows --- Release notes MEGAN /V5_2_0: --- - Rewrote DataProcessor algorithm to be more efficient - Rewrote parts of data parsing - Added ability to parse fastQ files for reads - More work on MeganServer capabilities (for internal use only) --- Release notes MEGAN /V5_1_5: --- - Fixed bug that caused magnitude values to be ignored when parsing RAPSearch2 files - Fixed a number of bugs --- Release notes MEGAN /V5_1_4: --- - Fixed new bug that sometimes caused parsing of files to partially fail due to a “invalid limit” exception - Fixed bug in alignment viewer that caused displayed unaligned sequence to be off by some positions - Added new collapse low supported nodes - Some work on SAM parser to support incoming alignment programs that generate SAM for BLASTN, BLASTX and BLASTP output --- Release notes MEGAN /V5_1_3: --- - Updated NCBI tree to latest version (downloaded on Jan 4, 2014) - Fixed newly introduced bug that prevented display of alignments - Other bug fixes --- Release notes MEGAN /V5_1_2: --- - prevent attempt to parse gzipped files and use “In memory” analysis of reads at the same time (as this doesn’t work) - fixed “null” exception in “enable taxa” menu item - fixed bug in “show match” command in alignment window - fixed bug in naming of file extensions in open file dialog --- Release notes MEGAN /V5_1_1: --- - Modified input parsers to support parsing of input files (such as BLAST files, reads files) in gzip or zip format. Specify e.g. as input.blast.gz or reads.fasta.zip - .megan files can now also be opened in gzip or zip format. --- Release notes MEGAN /V5_1_0: --- - First official non-beta version of MEGAN5 - This version does not expire - Contains a number of minor bug fixes - Fixed a number of bugs in the alignment viewer, including incorrect calculation of unaligned prefix sequence and selection problem --- Release notes MEGAN /V5_0_83-beta: --- - Fixed bug that caused MEGAN to report a problem in a SAM file where in fact there was no problem - Better presentation of SAM alignment in Inspector viewer - Support for SAM to contain raw score (using ZR:i:) and expected value (using ZE:f) - Support for SAM to contain reference length (using ZL:i) --- Release notes MEGAN /V5_0_82-beta: --- - Fixed bug in new command-line parser --- Release notes MEGAN /V5_0_81-beta: --- - Fixed bug in RDP Assignment details parser - Fixed bug related to using minimumTaxonCover - New command-line parsing code --- Release notes MEGAN /V5_0_80-beta: --- -fixed bug in SAM parser that prevented lines with query=* from being correctly parsed -fixed minor bug in /KEGG_ID parser --- Release notes MEGAN /V5_0_78-beta: --- - magnitude values are now read from blast file if no fastA file present - fixed enable-disable bug for Apply button in Import blast and reads - fixed bug that caused MEGAN to ignore expected values for RAPSearch2 input - expiry date set to end of the year, by then we should be out of beta testing! --- Release notes MEGAN /V5_0_77-beta: --- - Fixed bug that prevented BIOM import from working when unknown taxa encountered - Added Check for Updates menu item --- Release notes MEGAN /V5_0_76-beta: --- - Modified compare command to use multiple threads - Added support for reads with "magnitudes". These are weights assigned to reads. The read FastA header line must contain a statement of the form magnitude=55, magnitude|55, weight=55, or weight|55 for MEGAN to understand that the weight of the read is 55. This feature is turned on or off globally using the Edit->Preferences->Use Magnitudes menu item - Fixed a number of minor Chart-related bugs --- Release notes MEGAN /V5_0_75-beta: --- - Fixed bug that broke seed-name to count DSV export - Modified rarefaction analysis so as to report absolute numbers rather than percentages - Rarefaction algorithm changed so that values can only increase (sometimes used to dip) - Rarefaction algorithm on comparison files now uses minSupport of 10 - Fixed a number of minor bugs - Fixed bug that prevented MEGAN from recognizing RapSearch files that start with NO HIT --- Release notes MEGAN /V5_0_74-beta: --- - Modified command line option -h so that program reports usage and then quits - Added command line option -c that allows user to specify a file of commands to be executed in command-line mode - Fixed bugs present in some selection commands (and simplified selection code) --- Release notes MEGAN /V5_0_73-beta: --- - fixed bug in aligner that caused reference sequence to be incorrect in blastx-generated alignments - fixed bug in alignment exporter that caused %r tag in names to be ignored --- Release notes MEGAN /V5_0_72-beta: --- - Fixed bug in Radial Chart drawer - Added rotation menu items for Radial Chart drawer - Added command property that can be used to scale the Radial Chart drawer - Modified Show Assigned and Show Summarized commands so that individual numbers are show for all samples in a multi-sample document - Modified Save As MEGAN5 command so that all mapping files that have been set are used when upgrading classifications - Added navigation buttons to Import Blast dialog - Reduced some redundant code --- Release notes MEGAN /V5_0_71-beta: --- - Fixed bug in RAPSearch2 parser - Added property that allows one to extend the alignment viewer past the end of the alignment - FIxed large font issue in alignment viewer - Improved find command (to focus in string input rather than toggle find toolbar) --- Release notes MEGAN /V5_0_70-beta: --- - Modified RapSearch2 parser so as to correctly parse lines with NO HITS - Modified algorithms used in sample comparison dialog: - Use Normalized Counts now normalizes to 10 million reads. The manual describes how to change this value - Use Sub-Sample Counts now uses 1000 replicates for each sample, and then averages over the 1000 replicates. The manual describes how to change this value --- Release notes MEGAN /V5_0_69-beta: --- - Critical update. Fixed a major bug in the paired-end processor that caused counts of reads to be ridiculously high - Added example of how to use command-line version to capture counts for KEGG KO groups --- Release notes MEGAN /V5_0_68-beta: --- - Critical update (that is why this is a beta release): major bug in Kegg viewer prevented KO's from occuring below more than one pathway node - Added EC numbers to KO labels - Modified RapSearch2 parser to work with recent changes to RapSearch2 format (MEGAN is able to read both the old and the new .aln files) - Unified capitalization of commands and their parameters. Hopefully this won't break any scripts because most of the keywords are case-insensitive --- Release notes MEGAN /V5_0_67-beta: --- - Fixed two major bugs in Import Blast Dialog, so this update is essential - Simplified the Import Blast Dialog so that all input and output files are specified in a single tab rather than in three tabs --- Release notes MEGAN /V5_0_66-beta: --- - fixed major bug in blast import dialog that caused corrupt RMA files to be generated - fixed a number of bugs related to node selection in the kegg, seed and cog viewers - added choice of "assigned" or "summarized" counts when exporting taxonomic counts --- Release notes MEGAN /V5_0_65-beta: --- - Added support for RapSearch's NO HITS message - Fixed bug that caused incorrect scrolling of heatmap in KEGG and other viewers --- Release notes MEGAN /V5_0_64-beta: --- - Added new export command that allows one to upgrade MEGAN4 files to full MEGAN5 format --- Release notes MEGAN /V5_0_63-beta: --- - added "From file..." button to find tool bar and also modified KEGG, SEED and COG viewers so that the jtable on the left scrolls to the next found item --- Release notes MEGAN /V5_0_62-beta: --- - Fixed bug that prevented use of "change LCA parameters" menu item for very large datasets --- Release notes MEGAN /V5_0_61-beta: --- - parse gi numbers in the format (gi:123456789) - Fixed a number of minor bugs --- Release notes MEGAN /V5_0_60-beta: --- - Fixed bug that prevented alignment viewer from working --- Release notes MEGAN /V5_0_59-beta: --- - Fixed bug that prevented user from loading an alternative taxonomy - Fixed a number of small bugs --- Release notes MEGAN /V5_0_58-beta: --- - Added drop-down menu for user to explicitly set format of input blast file - Fixed minor bugs in CSV parsing - Renamed CSV (comma-separated value) menu items to DSV (delimiter-separated value) --- Release notes MEGAN /V5_0_57-beta: --- NOTE that MEGAN5 licenses issued before beta5-0-57 will not work with beta5-0-57 onward, due to a bug in the earlier version of licensing - Fixed bug which prevented MEGAN from using synonyms that end on a bracket --- Release notes MEGAN /V5_0_56-beta: --- - allow use of unregistered program with restricted functionality --- Release notes MEGAN /V5_0_55-beta: --- - Fixed bugs related to licensing - Fixed numerous minor bugs --- Release notes MEGAN /V5_0_54-beta: --- - MEGAN5 started open beta testing.