LAST CHANGES INTRODUCED IN THE PROGRAMME SEAVIEW 21_NOV_2021 ----------- - set to version 5.0.5 - Fix building with gcc 11 19_JUN_2020 ----------- - set to version 5.0.4 - Treerecs updated to version 1.2 11_JUN_2020 ----------- - set to version 5.0.3 - fix bug in "Save as PDF" with a tree in "circular" display mode. 19_MAR_2020 ----------- - set to version 5.0.2 - Accept extensions .fa .fst .fasta for FASTA files - macOS: stop reading preferences to find PhyML executable 26_FEV_2020 ----------- - set to version 5.0.1 - fix rare crash when reading fasta-formatted input file 24_FEV_2020 ----------- - allow kalign as external alignment algorithm - fix incorrect output in some border cases for Props/Statistics 19_JAN_2020 ----------- - Use retina resolution when copying tree to clipboard under macOS 28_DEC_2019 ----------- - Set to version 5.0 - seaview drives program "treerecs" to reconcile gene and species trees 27_NOV_2019 ----------- - Fix bug with -align -align_at_protein_level in presence of partial final codons 20_MAR_2019 ----------- - save preferences after default alignment method in Align menu was changed 02_MAY_2018 ----------- - set to version 4.7 - add new "Transfer Bootstrap Expectation" method 10_APR_2018 ----------- - set to version 4.6.5 - fix quite serious bug in GUI introduced in version 4.6.3 - add suboption -record_partition to option -concatenate in line command mode. 26_JAN_2018 ----------- - set to version 4.6.4 - improve detection of whether data file contains protein or nucleotide sequences 23_NOV_2017 ----------- - set to version 4.6.3 - fix typo in help file where option -align_extra_args was erroneously called -align_extra_opts - fix regression that prevented certain operations in command line mode - allow use on non-ASCII characters (e.g., CJK) in sequence names 12_JUL_2017 ----------- - set to version 4.6.2 - Restore drop-to-window of data file under MSWindows and when the desktop is scaled. 28_MAY_2017 ----------- - Unrooted tree drawing in SVG format: use accurate text length necessary with long names. 19_MAY_2017 ----------- - Fix bug when aligning at protein level and with command line a sequence ending with partial codon. 23_MAY_2017 ----------- - Unrooted tree drawing: make it accurate with very long names. 23_DEC_2016 ----------- - Save genetic code info also with FASTA format, and document it. 24_OCT_2016 ----------- - Tree drawing in SVG format: use the current zoom factor to enlarge the plot. 29_AUG_2016 ----------- - set to version 4.6.1 - better algorithm to compute DNA sequence consensus using IUPAC ambiguity codes 31_MAR_2016 ----------- - Added "trim rule" to control the display of long sequence names in phylogenetic trees 02_MAR_2016 ----------- - set to version 4.6 - fixed a bug that exchanged the NJ and BioNJ algorithms: ask for NJ, get BioNJ 12_OCT_2015 ----------- - added -usertree option to combine with -build_tree and -distance or -parsimony 15_APR_2015 ----------- - added "Show bootstrap trees" to parsimony, distance and PhyML, which opens a second tree window containing all bootstrap trees. 09_APR_2015 ----------- - added seaview.appdata.xml to present seaview in the GNOME and KDE software centers. 19_MAR_2015 ----------- - set to version 4.5.4 - added multiple-tree windows - added File/Save bootstrap replicates menu item 27_OCT_2014 ----------- - fixed error with command line -convert -output_format phylip - uploaded source code version 4.5.3.2 26_OCT_2014 ----------- - improved alignment display when using macintosh computers with retina display 24_SEP_2014 ----------- - fixed error in new method for computing tree root location 22_SEP_2014 ----------- - set to version 4.5.3 - now uses PHYLIP v3.696 with free license 17_SEP_2014 ----------- - fixed crash with command line operation: -align -align_at_protein_level 30_AUG_2014 ----------- - new rooting algorithm: root at middle of largest tip-to-tip distance 27_AUG_2014 ----------- - fixed crash with command line operation: seaview -align - Save patristic distances now operate on the subtree when there is one, and also computes the total tree length. - all seaview-created windows now have icons on X11 and WIN32 05_JUN_2014 ----------- - improved the file chooser dialog under linux+GTK that correctly redraws background FLTK windows 31_MAY_2014 ----------- - set to version 4.5.2 - use PHYLIP v3.695 to compute parsimony trees - can copy fasta-formatted sequences to an alignment window 06_MAY_2014 ----------- - fixed errors in "File" menu of tree windows after addition of new patristic distances item. 30_APR_2014 ----------- - added -remove_bootstrap command line option. - added -def_sites_selection command line option. 26_APR_2014 ----------- - set to version 4.5.1 - added many command line options to drive seaview without GUI. - added computation of patristic distances in the File menu of tree windows - modified the output of distance matrices that now also lists pairwise distances one per line 23_Mar_2014 ----------- - set to version 4.5.0 - pilot PhyML 3.1 - added several command line options to plot a tree in svg with colors and controlling outgroup 11_FEB_2014 ----------- - set to version 4.4.3 - fixed bug where aligned seqs were silently truncated if alignment is considerably longer than unaligned sequences. 26_NOV_2013 ----------- - Fixed error in the implementation of the -b2 option of Gblocks ("less strict flanking positions") The correct thing is to set -b2=tot_seqs/2 + 1. 16_JUN_2013 ----------- - set to version 4.4.2 - fixed bug under MSWindows with temporary files that caused problem when running several PhyML in parallel. - for Linux version, added optional use of GTK file chooser if available. 03_MAY_2013 ----------- - added a landscape option to the alignment printout function - modified the writing of MSF format according to the description of the MSF format in the doc of the TeXshade package. 18_APR_2013 ----------- - WIN32: added code so the seaview icon appears in the title bar of alignment and tree windows. 20_MAR_2013 ----------- - set to version 4.4.1 - fixed bug in statistics when using selected sites that were offset by one site 01_MAR_2013 ----------- - fixed problem when using Gblocks with sequences of varying length. 27_FEB_2013 ----------- - fixed problem when using Gblocks with very long sequence names where Gblocks did not run. 7_NOV_2012 __________ - fixed possible crash when using the mase format for files containing trees with @ in sequence names 19_SEP_2012 ___________ - replaced clustalw2 by clustal-omega - set to version 4.4.0 14_AUG_2012 ___________ Fixed crash when reading MrBayes or Beast-produced trees that contain loads of internal data. 29_JUN_2012 ___________ Version 4.3.5 - added options -plotonly and friends to plot rooted/unrooted trees in a pdf file. 22_MAY_2012 ___________ Version 4.3.4 - added threading for parsimony computation and opening of remote acnuc databases - FLTK 1.3.0 or above is now required - added Nucl/aa equilibrium frequencies option in PhyML dialog 16_JAN_2012 ___________ Version 4.3.3: - seaview now reads tree files output by MrBayes 3.2.0 6_DEC_2011 ___________ Version 4.3.2: - seaview now drives the Gblocks program to create site masks of blocks of evolutionarily conserved sites (see the "Sites" menu) 30_NOV_2011 ___________ Version 4.3.1: - Added the "Props/Statistics" command to compute base and amino acid frequencies. - Added the "Select" function to tree windows that allow to select species in the tree and have them become selected in the corresponding alignment window, and vice-versa. 20_JUL_2011 ___________ Version 4.3.0: the new FLTK 1.3.0 is now used to build the GUI (seaview remains compatible with FLTK 1.1.*). There is now a print command for tree plots under Linux/Unix. 16_JUL_2011 ___________ PostScript output: the page format (A4/Letter) is recognized by evince viewer. 12_JUL_2011 __________ Added new genetic code #24 for Pterobranchia mt. 23_JUN_2011 __________ Added SVG output for tree plots. Unix/Linux: Use the directory containing an open file when using save as. 22_JUN_2011 __________ Fixed bug where "File/Save selection" would change the format of next "File/Save" commands. 28_APR_2011 ___________ Seaview now highlights the name of the cursor-containing sequence. 12_APR_2011 __________ Fixed alignment bug that crashed seaview when aligning gap-only sequences. 23_MAR_2011 __________ Fixed error in MtArt model name that prevented using this model. 28-JAN-2011 __________ Version 4.2.12: corrected bug in "Sites" menu operations. 25-NOV-2010 __________ Version 4.2.11: Sites menu: hide and change of site line now save current site choice; Save sites operation was removed. 23-NOV-2010 __________ Fixed bug in profile alignment if profile contains gap-only sites or if profile contains mixed-case data. 03-NOV-2010 __________ Version 4.2.10: Fixed bug in bootstrap parsimony where only the first tree of all equally parsimonious ones was used. Added time-based seeding of random numbers. 25-OCT-2010 __________ Version 4.2.9: Added drag & drop of alignment file to empty seaview window under X11. Fixed Mac OS X 10.4 i386-specific bug in pseudoterminal. Modified Makefile to add -lfontconfig to link command. 11-OCT-2010 __________ Version 4.2.8: Added check that aligned sequences don't contain unexpected characters 09-OCT-2010 __________ Don't show codon-based and variability-based regions in view_as_prots mode. 28-SEP-2010 __________ Version 4.2.7: Fixed use of ? as unknown state when aligning. After profile alignment, propagate profile gaps to site choices. Delete temporary PhyML files created when using bootstrap. 28-AUG-2010 __________ Version 4.2.6: Mac OS X: Fixed run_external_prog_in_pseudoterm that did not work with 10.4. Fixed consensus bug when no nucleotide in any sequence. Fixed reroot bug with PhyML alrt/bootstrap value. 06-MAY-2010 __________ Version 4.2.5: Allow pdf output with non ascii pathname. Use FLTK v1.3 with printing support with Mac OS X and WIN32. Allow seq order change during phyml run, and forbid several simultaneous phyml or alignment runs. 01-APR-2010 __________ Version 4.2.4: Fixed memory allocation bug in customization 22-FEB-2010 __________ Version 4.2.3: When back to DNA from protein view, better handling of remaining partial codons 04-JAN-2010 __________ Version 4.2: added cladogram tree display + copy selected sequences to clipboard 22-JUN-2009 __________ Version 4: Seaview can now compute and draw parsimony, distance and PhyML phylogenetic trees 22-OCT-2008 __________ Version 3.2: Database import can be done using a keyword 08-OCT-2008 __________ Version 3.1: now use Fl_Native_File_Chooser 11-SEP-2008 __________ Version 3.0: sequences can be imported from embl, genbank, swissprot if internet access 04-MAR-2008 __________ Version 2.4: PHYLIP format: user can customize the max length of names 22-FEB-2008 __________ Version 2.3: corrrected bug if adding/deleting/moving sequences when in 'view as proteins' mode 2005-2007 --------- lost list of changes for this period 24-MAY-2005 __________ change in function what_format of file use_mase_files.cxx to allow new MSF format. 6-APR-2005 __________ - Added pdf output in menu "File"" by use of the PDFLib Lite library, which must be installed before trying to compile and link seaview (get it at http://www.pdflib.com/products/pdflib/download-source.html). - Changed customization through "Props:Customize" menu item that allows all changes to be doable through the GUI. - Customization is no longer achieved through X11 resources but by reading/writing file $HOME/.seaviewrc - the WIN32 version uses native MSWindow's file dialogs. added 2 source files: pdf.cxx custom.cxx changed source files: seaview.cxx, seaview.h, resource.cxx, chooser_plus.cxx, mac_pc_extras.cxx, use_mase_files.cxx, old_file_chooser.cxx, nexus.cxx 20-DEC-2004 ----------- remove no longer useful file seaview.linuxPC.gz changed executable file: seaview.SOLARIS.Z 17-DEC-2004 ----------- Use a gzipped-tar file for the linux-on-PC distribution (seaview.linuxPC.tgz) containing the executable, an example file, the help file, the clustalw executable and the seaview_align.sh shell used by the align command. changed executable files: seaview.linuxPC.tgz 16-DEC-2004 ----------- - Base coloring rule on the 'datatype=dna|protein' information present in an input nexus file rather than on the guessing algorithm used for other file formats. - Let ? characters unchanged when using the nexus format - Allow for syntax "name=from-to\3" when defining a charset in a nexus file. changed source files: seaview.cxx, seaview.h, nexus.cxx, seaview.tar changed executable files: seaviewWin95.exe, seaviewMAC.hqx, seaviewALPHA.tgz, seaview.linuxPC.gz