Release: v5.1.0 (12June22)

Release: v5.0.8 (1June22)

1. A new option "Concat" has been added; when this is unchecked, it will not create a concatenation of the first genome to run against all chromosomes of the second, instead it perform a chromosome-by-chromosome search.
2. MUMmer4 can be used by compiling it on your machine from the /ext directory and adding its path to the "symap.config" file. See Running MUMmer.
3. When computing alignment&synteny, all stacktrace errors are now written into error.log.
4. The database name is prefixed to the "logs/LOAD.log" file name.
5. A new document has been created for when there is problems running MUMmer from SyMAP.
6. ConvertNCBI script was writing the scaffold sequences to end of the last chromosome (this did not make the annotation or synteny wrong - just extra sequence).

Release: v5.0.7 (4Feb22)

1. MUMmer has been updated since the last SyMAP release; the code in the /ext/mummer4 directory has been updated for the latest MUMmer. The documentation has been updated accordingly (see Running MUMmer).
2. ConvertNCBI: (1) Include ncbi_dataset format. (2) Convert hex to character.
3. Parameters: (1) The Load would not work if any numeric parameter was set to blank. (2) For Alignment&Synteny "Parameters", the Global button was removed as it did not work except under weird conditions.
4. Help: the viewer Help pages link to the pages at www.agcol.arizona.edu/software/symap. The approach for Mac was becoming obsolete, so it was changed. For Linux, more supported browsers were added.
5. Improve documentation.
6. Developers: Removed all Applet code (was disabled previously, but code was in everything).

Release: v5.0.6 (2June20)

1. Some changes were necessary for SyMAP to run with MySQL v8.
   • The schema needed a change, which will occur on first reading of database.
2. SyMAP works on MacOS Catalina 10.15
   • It checks each external program to see if it is executable, as this is not automatic with 10.15 (see Trouble Shoot External Programs).
3. SyMAP can be compiled with Java v14 (some changed were necessary for this).
4. The Applet has been removed and will no longer be supported. (It is in earlier SyMAP versions, and can be obtained at github).
5. The built-in MySQL database on Linux is no longer supported.
6. The Alignment&Synteny has a couple checks for 'ordered_against' before processing: (1) Is the order_against the same as the other selected project. (2) Does the ordered directory already exist.

• Load Annotation
  • In the Params interface for a project, the user can set what keywords from the column 9 "Attributes" field of the gff file to load; this was not working correctly and has now been fixed.
  • The type (column 3) of mRNA was being loaded as a gene, which causes duplicate records; now mRNA's are ignored.
• Alignment & Synteny
  • Though it was not possible to make MUMmer v4 part of SyMAP, it is possible to install MUMmer v4 in the /ext/mummer directory and it will work. Instructions are provided in System Guide.
  • The nucmer "--maxmatch" parameter was automatically used for self-synteny when a sequence file was being compared with itself; this would result in an extremely long execution time for large files (e.g. chromosomes). Consequently, this parameter has been removed, but can now be set by the user in the "Parameter" interface.
  • Pair Parameters: (1) The user can set parameters in "Self Args", which are only used when a chromosome sequence is being compared to itself. (2) This interface was very confusing as to when parameters were saved and what would be used; this should be clearer now, and is explained in the "Help" for the Parameter interface.
  • If only part of the alignments finished and it ended pre-maturely, when run again, it will not redo any finished alignments.
• Internally, goobs of commented out code has been removed.

Release v5.0 (22jan20)

• General
  • Error messages (and stack traces) are written to error.log
  • There was one symap script with various flags, now there is four symap scripts with less flags, as follows:

    Script	Build	View	Has 3D view
    ./symap	Yes	Yes	No
    ./symap3D	Yes	Yes	Yes
    ./viewSymap	No	Yes	No
    ./viewSymap	No	Yes	Yes

  • The symap -c command line parameter can be used to specify a configuration file other than 'symap.config'
  • The Summary list of all selected projects has been enhanced.
• Query database
  • The "Display for Selected Pair:" popup Summary is now available for self-synteny and FPC-Seq
• Build database
  • Log files: The log files are no longer in the results directories, instead they are in the top level /logs directory, as follows:
    1. The output from the loads are concatenated to the file /logs/LOAD.log.
    2. The output during alignment is in the /logs/<proj1-to-proj2> directory.
    3. The output to the terminal from the alignment and synteny computation is written in the /logs/<proj1-to-proj2>symap.log file.
  • Load project
    • The input files can be gzipped (end with .gz)
    • The Parameters menu uses the previous location for the file/directory finder.
    • Add ConvertEnsembl.java to convert an Ensembl file to SyMAP annotation file.
  • Alignment & Synteny
    • The trace output to terminal is much more informative.
    • The alignments for self-synteny have been optimized, which also changes the results (e.g. demo_seq now has some tiny blocks were before it had none).
    • The number of CPUs can be set in the interface, or either of the following:
      1. Use the -p command line parameter, e.g. ./symap -p 12.
      2. Set the 'nCPUs' configuration parameter in the symap.config file, e.g. nCPUs=12.
    • Much of the code for building the syntenies has been re-written, but the results are basically the same with a few tiny differences.
  • Directory structure: The following are the directory changes, where they are under /data.

    New	Old	Description
    /seq	/pseudo	Directory for sequence projects
    /seq/<project>/sequence	/pseudo/<project>/sequence/pseudo	Default directory for sequences
    /fpc_results	/fpc_pseudo	Directory of FPC to sequence project results
    /seq_results	/seq_pseudo	Directory of two sequence project results
    /seq_results/<proj1-to-proj2>/align	/pseudo_pseudo/<proj1-to-proj2>/anchor	Directory of alignments

• A few more improvements on the applet code.
• Renamed some functions to make them clearer and updated the help.
• Improved the Help on the parameters page.
• Fixed a rare memory bug (occured on a self-synteny; requires the database to be re-created).
• The Image button does not work for Java v9, so a popup tells the user.
• Added a Java script called ConvertNCBI.java, as documented in NCBI to SyMAP.

• The applet code has been fixed to work better.
• The FPC to sequence block view had a bug that was fixed (though 'reverse' does not work).

• There was a limit of 75 sequenced regions per genome, which the block view did not work after that.
  The limit has been changed to 150 and a popup message occurs if that limit is passed.
  A script (scripts/lenFasta.pl) is supplied to provided the sorted lengths, where you should set the min_size parameter to the 150th length.

• Fixed problem that prevented symap from running with new JDK v9.

• Fix display sizing errors in circle view display
• Fix database error for long project names (max project name remains 40)

New Features:

• New, unified web access applet interface. Now you can present a unified SyMAP web display of some or all of the projects in your database using just one small HTML page (no CGI). Applet interfaces are also available for each of the sub-functions (dotplot, circle view, etc.) enabling customized web displays.

Modified Features:

• The Explorer has been updated to be more usable for draft projects, i.e. when there are many sequences that have not been ordered and anchored to pseudomolecules. Specifically, it will now show up to 450 sequences, and to decrease clutter it shows only sequences that actually have a synteny block.
• The prior web system files have been removed, including the cgi and supporting perl modules.
• The circle view now draws all text labels horizontally, due to rendering problems with rotated text on several platforms (most severely on Mac). The rotated text is still available through a checkbox option. It is no longer necessary to run the perl install script to install web functionality.

New Features:

• Publication-quality image saving. A save button has been added to every graphical window allowing saving to a wide variety of formats, including scalable vector formats (svg, eps, pdf) which may be resized clearly to any size. (Many thanks to the developers of the FreeHEP Vector Graphics library, and especially Mark Donszelmann, for making this possible!)
• Download of block co-ordinates. Choose the species of interest, open the Explorer, and the download button is at the lower left.

Modified Features:

• Applet is signed with a DigiCert certificate, removing the security blocks which have been increasing in recent Java versions.
• MUMmer binaries for Mac OSX have been replaced by 64-bit versions. The 32-bit versions which had been supplied could not access more than 2G RAM, preventing alignment of many chromosomes.

Version 4.0
Release date: 7/15/2012

New Features:

• Project Manager Enhancements
  • Create new projects through the Manager
  • No need to create directories or copy files
  • Alignment & Synteny parameters also available
• Query Page Enhancements
  • Compute putative gene families across species
  • Many additional filters
  • Create and view Muscle multiple-alignment for selected results
• Additional Features
  • Script 3track_figure.pl makes 3-genome figure for publication (see online Tour; script added to 4.0 package post-release)

Modified Features:

• Write contig anchoring information to a file (order_against mode)
• No longer creates the "_ordered" project output from order_against
• grp_prefix parameter now optional (but recommended). grp_sort eliminated.
• Self-alignments improved by using -maxmatch option of MUMmer for individual chromsome self-alignments
• Top-2 filtering modified to accept also hits within 80% of the 2nd best score, in order to retain gene-family hits and allow identification of families through the query interface.

Version 3.5
Release date: 1/24/12

New Features:

• Dynamic circular display
  • Circular-style view allowing addition/removal of species and chromosomes
  • Replaces 3D view in the web applet (removing problems of MacOS support for 3D)
  • 3D still available in standalone mode
• Annotation query interface (Java-based, upgrades the web CGI version)
• Project parameters editing window
• Unsigned web applet (no approval popups, if database and webserver have same host)
• For draft sequence using order_against, create ordered and anchored versions of the project

Modified Features:

• Added contig-flipping to draft sequence order_against function
• Added draft sequence ordering demo
• Improved command-line launch script

Version 3.4
Release date: 12/14/10

Modified Features:

• Query files catenated before running MUMmer, for substantial increase in speed.
• Batch alignment buttons added to Project Manager.
• Improvements to handling of unordered scaffolds, including:
  • Scaffolds can all be in one fasta file.
  • Added min_size parameter, to specify minimum size scaffold to load.
  • Added order_against parameter, to specify reference sequence for ordering scaffolds (the order only affects the dotplot display)
• Minor changes to CGI page displays to better accomodate unordered.
• Fix compilation error in 64-bit MUMmer binary, which prevented use of very long pseudomolecules.

Version 3.3
Release date: 10/4/10

Modified Features:

• Added "no_overlapping_blocks" parameter
• Added printout of block and synteny anchor tables to "/results" directory
• Remove "Contig0" (singleton clones) from FPC displays
• Adjustments to unannotated sequence clustering to obtain larger clusters, not dependent on the order of scanning of MUMmer output files.
• When clicking a block in the dot plot, 2D view will open with hit filter setting "show only synteny hits"
• Some bug-fixes to search.cgi