Current Windows 10,8,7 Release Version: DNA Alignment 1.3.3.2, released 2020 January 18
Alternative Windows XP Release Version: DNA Alignment 1.3.3.2, released 2013 December 24
Improvements from version 1.3.3.1 to version 1.3.3.2:
1. Fixed numerous screen issues (esp. auto-sizing of texts, auto-sizing of layouts on various displays).
2. Enhancement: Display of the reference sequence name above the reference sequence.
3. Enhancement: For long/short sequence names: Slider for increasing/decreasing the displayed width of the sequence names.
4. Enhancement: in Load/Save dialog, existing file names with different file type can be displayed using the "all file types" filter.
Known issues in DNA Alignment 1.3.3.2:
1. When using "Add alignment" repeatedly (to import an aligment [*.ali] file into the current session), imported indels are duplicated. We found this issue also in version 1.3.3.1. Work-around: check if new indels were inserted into the reference sequence, and resolve the duplication with manual editing (right-click a cell, or use the keyboard's delete key).
2. In "Amino acid" mode, the reference sequence is not initially positioned correctly over the sequence table. Work-around: adjust the sequence name column width slider.
3. In "Amino acid" mode, after saving and exiting a session, then loading a file, scroll bars may not be displayed. Work-around: exit software, restart software, load file.
Improvements from version 1.3.1.1 to version 1.3.3.1 (versions 1.3.2.0 and 1.3.3.0 were not released):
1. New Function: "Add alignment file" allows an ali-file of previously aligned sequences to be imported into the currently loaded set of sequences. This implies that the same reference sequence was used in both cases. On import, gaps are introduced into the sequences as required.
2. Fixed: DNA Alignment can now save into work folder path names that contain multiple dots, e.g. C:\Users\user11.uni-kiel.000\Desktop\temp
3. Fixed in Network 4.6.1.1: DNA Alignment may generate "Network 4.5 rdf" files with sequence names longer than 15. Network now imports these files without error messages and automatically generates unique short names.
4. Fixed: Previously, auto-alignments generated too many insertions in some data sets: Now, base changes are more likely, insertions less likely than in previous releases. The default alignment parameters are now (5,15), previously they had been (4,10).
5. Enhancement: There are two new checkboxes for improved auto-alignment of FASTA sequences which already contain Ns or gaps: These can be accessed from the start screen as follows: Parameters / Adjust: Ignore Ns in FASTA sequences, Ignore gaps in FASTA sequences. Both options are checked by default. The parameter settings for auto-alignment are now saved into the UserSettings.txt file.
6. Enhancement: FASTA file comment lines (starting with '#') are now allowed. These comment lines are ignored when the sequences are loaded.
7. Enhancement: When using the keyboard, there are now the standard keyboard shortcuts CTRL+Z (to undo the last change) and CTRL+S (to save). Also, there is a new cursor movement mode switch between "stay in cell" and "move right to next cell".
8. Enhancement: In Save / Network 4.5 binary data format rdf (*.rdf), there is now a warning message if there are 1 or more multistate characters which have been (greedily) binarised.
Improvements from version 1.3.0.1 to version 1.3.1.1:
1. Fixed: Amino Acid mode, Load Fasta file(display only), when loading files with gaps.
2. New Function: Find motif.
3. New Option: "Load (auto align auto reverse)" for dna and amino acid sequences with unknown orientation (slower than normal auto-align).
4. New Parameters: For more user-control over the auto-alignment. To keep the old alignment behaviour, use the default parameter values (4, 10).
Improvement from version 1.3.0.0 to version 1.3.0.1:
1. Fixed: window auto-fit for "wide" displays (used increasingly in new laptops).
Improvements from version 1.2.0.0 to version 1.3.0.0:
1. Export multistate amino acid files for Network as *.ami instead of *.rdf. (Previously had to be renamed to *.ami for Network)
2. New version of *.rdf and *.ami for Network 4.5, saves faster. Data may still be saved in the old *.rdf and *.ami formats.
3. The new binary *.rdf saves no "N" but instead simply a "1" where there is a nucleotide difference to the first sequence, regardless of whether this is a multi-state position or not. This is an alternative to the binarisation in the old *.rdf, not a replacement.
4. Improved the new multi-alignment optimisation of the last 20 nucleotide positions, so that more sequences than before are optimised.
5. Added website help pages for binary *.rdf, and for publication-style tables (*.txt).
Improvements from version 1.1.3.0 to version 1.2.0.0:
1. Enhanced auto-align for improved alignment in the last 20 columns, when more than 1 sequence is considered. As in previous software versions, the pairwise alignment algorithm is based on DIALIGN [Morgenstern B et al. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics. 1998;14(3):290-4] with our own speed optimisations. In software version 1.3.0.0 we further optimise the alignments by comparing multiple sequences.
2. Help menu now available before and after a file is loaded. No more "Question" window for "Load (auto-align)".
Improvements from version 1.1.2.9 to version 1.1.3.0:
1. Fix for rare problems when loading reference sequence or fasta files.
To avoid problems, the file "Interim_Sto.txt" is now created in the reference sequence load directory and the fasta file load directory.
2. New option to configure display colours ("Settings / Display parameters", "Settings / Save"). These settings are saved in the software installation directory in the file "UserSettings.txt". The default display colours were changed to light, pastell colours. Users who prefer the cheerful colours from the previous software versions can rename the file "UserSettings_classic.txt" to "UserSettings.txt".
3. Change of highlighting of alignment table cells: Previously: ambiguous cells (e.g., in DNA mode, M = A or C) were not highlighted if the ambiguity included a match (exception: N = A, C, G, or T, in DNA mode). New: all ambiguous cells are highlighted because they are a potential source of error which needs to be investigated.
Please keep the Help website to yourself.
