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  ID ▼ Type ▼ Status ▼ Priority ▼ Milestone ▼ Owner ▼   Summary + Labels ▼ ...
  157 ---- Accepted High Release2.0 ggvai...@gmail.com   0% distances not working  
  73 Defect Accepted High Release2.0 ggvai...@gmail.com   Nexus export silently truncates long names   NexusFile MegaFile Usability  
  134 Defect Accepted High Release2.0 ggvai...@gmail.com   Need to support Nexus' "consists-of-every-third-position" character sets.  
  168 ---- Accepted High Release2.0 ggvai...@gmail.com   Taxonsets is pretty weird  
  169 ---- Accepted High Release2.0 ggvai...@gmail.com   TNT export where the column names contain ')' have issues  
  105 Defect Accepted High ---- ggvai...@gmail.com   Complete Overlap will not count sequences without species names   CompleteOverlap SpeciesIdentifier  
  120 Defect Accepted High ---- ggvai...@gmail.com   Export of Moleculomorph datasets dodgy   Export Morphology  
  142 Defect Accepted High ---- ggvai...@gmail.com   SM not reporting intergeneric pairwise distances   SequenceMatrix  
  149 ---- Accepted Medium Release2.0 ggvai...@gmail.com   Mega should *always* export with underscores, not spaces  
  88 Task Accepted Medium Release2.0 ggvai...@gmail.com   Check all major import variants   SequenceMatrix Compatibility  
  93 Enhancement Accepted Medium Release2.0 ggvai...@gmail.com   TNT and Nexus exports need to support different types of gaps   SequenceMatrix Nexus TNT gaps  
  106 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Problems with TaxonSet names   SequenceMatrix Exporter Taxonsets  
  116 Enhancement Accepted Medium Release2.0 ggvai...@gmail.com   Handle Sequence name/species name situation with SeqMat better   SequenceMatrix  
  117 Defect Accepted Medium Release2.0 ggvai...@gmail.com   SeqGrid exports won't expand sequences   TaxonDNA Nexus TNT  
  118 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Nexus import fails if semicolon on the same line as last sequence   Nexus  
  125 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Nexus export should occur in the order on the main window  
  126 Defect Accepted Medium Release2.0 ggvai...@gmail.com   A whole lot of Pairwise mode/Correlation mode bugs. Also numbers!  
  128 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Reset the colour coding on pairwise threshold, so that the range can be "shortened" from the UI.  
  130 Defect Accepted Medium Release2.0 ggvai...@gmail.com   File export loading issue  
  135 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Export table (as tab delimited) will have to be majorly smartified  
  136 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Internal gap load/export needs cleaning up/  
  137 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Probably bug with the AICC calculation in correlation mode.  
  140 Defect Accepted Medium Release2.0 ggvai...@gmail.com   File loading needs to be much improved  
  141 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Pairwise mode behavior with a single column is incorrect (?)  
  162 ---- Accepted Medium Release2.0 ggvai...@gmail.com   PDM: Can't uncancel distances  
  163 ---- Accepted Medium Release2.0 ggvai...@gmail.com   "Clear All" leaves one sequence in the table  
  165 ---- Accepted Medium Release2.0 ggvai...@gmail.com   You should be able to cancel all the sequences in a column in one shot  
  170 Enhancement Accepted Medium Release2.0 ggvai...@gmail.com   BLAST sequences on NCBI to look for oddities  
  171 Defect Accepted Medium Release2.0 ggvai...@gmail.com   Clean up Nexus output UI  
  172 Enhancement Accepted Medium Release2.0 ggvai...@gmail.com   Colour-code the positional information  
  132 Defect Clarification Medium Release2.0 ggvai...@gmail.com   Export no-data into Excel as 'zero' so it's easier to work with.  
  43 Defect New Medium ---- ggvai...@gmail.com   SequenceMatrix should be able to work around the weird columns-not-displayed bug.   SequenceMatrix Portability  
  79 Enhancement New Medium ---- lailaizh...@gmail.com   Export sequences having Large distances  
  122 Enhancement Accepted Medium ---- ggvai...@gmail.com   Modify SequenceMatrix to accept unaligned data   Usability  
  30 Enhancement Accepted Medium ---- ggvai...@gmail.com   Exporter should be able to export 'genus species' only (no GI number)   Exporter  
  31 Defect Accepted Medium ---- ggvai...@gmail.com   GenBankExplorer should have an invert-selection command   GenBankExplorer Selection Usability  
  60 Defect Accepted Medium ---- ggvai...@gmail.com   Too easy to cover up labels in undersized windows   Usability UserInterface AWT  
  64 Enhancement Accepted Medium ---- ggvai...@gmail.com   Each SpecId component should have it's own Export button   Usability  
  69 Defect Accepted Medium ---- ggvai...@gmail.com   Complete Overlap: Export All doesn't print headers properly in 'cut off ...' mode   CompleteOverlap  
  77 Enhancement Accepted Medium ---- ggvai...@gmail.com   SpeciesIdentifier should be able to use '_' as ' '.   Usability Fasta  
  80 Defect Accepted Medium ---- ggvai...@gmail.com   K2P distances don't quite correspond with any other program   Testing  
  83 Enhancement Accepted Medium ---- ggvai...@gmail.com   PairwiseExplorer should export all (intra and inter) pairwise distances, including species names   Feature PairwiseExplorer  
  85 Enhancement Accepted Medium ---- ggvai...@gmail.com   PDM should allow you to use either ranks or normalised pairwise distance to do colors   PDM SequenceMatrix  
  92 Enhancement Accepted Medium ---- ggvai...@gmail.com   Custom taxonsets   Taxonsets  
  97 Defect Accepted Medium ---- ggvai...@gmail.com   Opening a file while in Correlations mode doesn't show results of the correlation analysis   SequenceMatrix CorrelationMode  
  101 Defect Accepted Medium ---- lailaizh...@gmail.com   Double counting in Pairwise explorer  
  104 Defect Accepted Medium ---- ggvai...@gmail.com   GenBankExplorer doesn't understand 'X^Y' or 'X.Y' locations   GenBankExplorer GenBankFile  
  107 Enhancement Accepted Medium ---- lailaizh...@gmail.com   Automatic removal of sp. aff. af. cf. cff. n. (Unidentifed species)   SpeciesIdentifier  
  109 Defect Accepted Medium ---- ----   Could not interpret location 'AY532815.1:<1..445':   GenBankExplorer  
  113 Enhancement Accepted Medium ---- ggvai...@gmail.com   Export to Hennig86/Malign  
  114 Defect Accepted Medium ---- ggvai...@gmail.com   Pairwise distances inaccurate for internal gap-non internal gap comparisons   TaxonDNA PairwiseDistance  
  127 Defect Accepted Medium ---- ggvai...@gmail.com   Multi-taxon selection in the Window  
  139 Defect Accepted Medium ---- ggvai...@gmail.com   Fix the ugly Java Swing window used by JFileChooser in UI.DirectoryInputPanel.java  
  129 Defect Clarification Medium ---- ggvai...@gmail.com   Individual file does not open: but works-for-me now, checking with Farhan.  
  18 Enhancement Longterm Medium ---- lailaizh...@gmail.com   Search function in TaxonDNA   TaxonDNA2.0 Search  
  154 Enhancement Accepted Low Hennig2009 ggvai...@gmail.com   Allow merging of rows  
  153 Task Accepted Low Hennig2009 ggvai...@gmail.com   TNT Taxonset limits  
  119 Defect New Low Release2.0 lailaizh...@gmail.com   Cancel button in Sequence Matrix doesn't work  
  148 Enhancement Accepted Low Release2.0 ggvai...@gmail.com   Phylip input/output support  
  152 Task Accepted Low Release2.0 ggvai...@gmail.com   Check the transversion calclations on the sequencematrix.  
  27 Defect Accepted Low Release2.0 ggvai...@gmail.com   RightLayout can't handle FILL_x except on the rightmost component on the line  
  89 Enhancement Accepted Low Release2.0 ggvai...@gmail.com   Refer to the 'reference taxon' as the 'outgroup'.   Usability SequenceMatrix  
  90 Enhancement Accepted Low Release2.0 ggvai...@gmail.com   0% distances in SequenceMatrix should colour by clusters   Usability SequenceMatrix  
  115 Defect Accepted Low Release2.0 ggvai...@gmail.com   You need to run 'ant clean' before 'ant release'   Build  
  123 Enhancement Accepted Low Release2.0 ggvai...@gmail.com   Remove gaps during export?   Feature Dunno  
  151 ---- Accepted Low Release2.0 ggvai...@gmail.com   Find 0% distances should allow you to break things down by gene  
  161 ---- Accepted Low Release2.0 djloh...@gmail.com   Log name changes for species  
  110 Defect New Low ---- lailaizh...@gmail.com   Inaccurate Best-close-Match threshold rounding up   SpeciesIdentifier  
  16 Defect Accepted Low ---- ggvai...@gmail.com   MegaFile can't handle sequences which have been commented out   MegaFile  
  25 Defect Accepted Low ---- ggvai...@gmail.com   AlignmentHelper has various limits on sequence processing   AlignmentHelper Clustal  
  28 Enhancement Accepted Low ---- ggvai...@gmail.com   Nexus support needs to be stricter   Nexus  
  86 Defect Accepted Low ---- ggvai...@gmail.com   CDM doesn't work as coded   SequenceMatrix CDM  
  87 Defect Accepted Low ---- ggvai...@gmail.com   Bug: On test dataset, Gluma musgravia is always given a very low score   TestCase SequenceMatrix CDM  
  103 Defect Accepted Low ---- ggvai...@gmail.com   Total correlation calculations off?   CorrelationsDisplayMode SequenceMatrix  
  8 Defect Longterm Low ---- ggvai...@gmail.com   Catch (and deal with) all OutOfMemory exceptions  
  9 Defect Longterm Low ---- ggvai...@gmail.com   TaxonDNA holds locks on files too long  
  14 Enhancement Longterm Low ---- ggvai...@gmail.com   Upgrade BrowserLauncher to BrowserLauncher2  
  17 Enhancement Longterm Low ---- lailaizh...@gmail.com   Selection of multiple sequences   SequenceSelection MultipleSequences ambitious  
  144 ---- New ---- Release2.0 ----   K2P failures  
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