| 1 | ARB change log |
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| 2 | |
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| 3 | Major changes for next release: |
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| 4 | |
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| 5 | - DNA realigner |
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| 6 | * several unjustified failures will no longer happen (fixes #419 and most likely #145) |
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| 7 | - correctly re-syncs after 'X' (if possible at all) |
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| 8 | - no longer fails for 'B' and 'Z' |
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| 9 | - accepts 3 or more consecutive IUPAC codes in DNA |
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| 10 | * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed) |
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| 11 | * fixed several minor bugs |
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| 12 | - expand zombies in tree (unfold groups) |
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| 13 | - external (command line) aligners: |
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| 14 | * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type |
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| 15 | * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment |
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| 16 | * no longer ask what to do with aligned sequence, just overwrite it |
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| 17 | - only warn about real sequence changes (so please do NOT ignore from now on!) |
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| 18 | - updated/added external tools: |
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| 19 | - added alternate RAxML (DNA only; version 8.0.26) |
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| 20 | |
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| 21 | Fixes for arb-6.0.2 (8 Aug 2014): |
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| 22 | |
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| 23 | - compile issues on Snow Leopard (OSX 10.6) |
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| 24 | - merge Debian security fix for CVE-2008-5378 |
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| 25 | - small changes to build system for Debian |
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| 26 | - add desktop integration files |
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| 27 | |
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| 28 | Fixes for arb-6.0.1 (22 Jul 2014): |
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| 29 | |
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| 30 | - arb_parsimony |
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| 31 | - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group) |
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| 32 | - corrected branchlength calculation for "Add marked partial species" |
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| 33 | - dots were treated as gaps for protein sequences (now treated as 'X'; analog to DNA treating gaps as 'N'). thx to Yan Shi for detecting that problem! |
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| 34 | - print |
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| 35 | - preview failed (showed empty postscript file) |
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| 36 | - print to file now always saves in user home |
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| 37 | - raxml (import tree with bootstrap values) |
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| 38 | |
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| 39 | |
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| 40 | Major changes for arb-6.0 (4 Jun 2014): |
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| 41 | |
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| 42 | - merge databases allows to |
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| 43 | - merge from an existing database into the database loaded in ARB_NT |
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| 44 | - merge to existing databases from the database loaded in ARB_NT |
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| 45 | - ARB can now |
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| 46 | - be restarted with another database and |
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| 47 | - a second instance of ARB can be opened |
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| 48 | - ARB_DIST |
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| 49 | - Detect clusters of species with similar sequences (OTUs) |
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| 50 | - allow automatic recalculation of matrix and/or tree whenever some parameter or |
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| 51 | data changes (only makes sense for smaller species sets) |
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| 52 | - extract distance matrix from tree |
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| 53 | - Rewrote chimera check. Allows filtering |
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| 54 | - added RNACMA (computes clusters of correlated positions) |
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| 55 | - PT-Server |
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| 56 | - changed behavior |
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| 57 | - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment) |
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| 58 | - reports previously missing hits in joined genes |
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| 59 | - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible |
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| 60 | matches that go beyond the end of the sequence) |
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| 61 | - dots in the middle of the alignment act like the sequence ends there |
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| 62 | - minimum probe length reduced to 2 (was 6) |
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| 63 | - allow up to 50% of probe to mismatch |
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| 64 | - performance |
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| 65 | - optimized memory-estimation (will build in fewer passes) |
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| 66 | - uses any number of passes (not only 1, 5, 25, ...) |
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| 67 | - allows to define used memory by setting environment variable ARB_MEMORY |
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| 68 | - reduced memory needed to build/run ptserver (approx. 50%) |
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| 69 | - reduced size of indexfile (.pt) to ~50% |
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| 70 | - fast startup of existing ptservers |
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| 71 | - probe design |
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| 72 | - faster in many cases |
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| 73 | - allow to design probes of length 8 (previously 10) |
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| 74 | - allow to design probes with different lengths (specifying min/max length) |
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| 75 | - fixed number of outgroup hits reported when decreasing temperature |
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| 76 | (now each outgroup member only occurs once) |
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| 77 | - show possible reasons why no probes could be designed |
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| 78 | - probe match (allow any number of mismatches) |
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| 79 | - next relative search |
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| 80 | - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences) |
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| 81 | - corrected and improved scaling of relative scores |
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| 82 | - more accurate scores (due to fixes in PT-Server; see below) |
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| 83 | - faster in many cases |
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| 84 | - show errors from ptserver build in ARB |
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| 85 | - fast-aligner |
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| 86 | - searches next-relatives based on selected column-block |
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| 87 | - align multiple column-blocks based on SAI |
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| 88 | - Rewrote alignment adaption during merge |
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| 89 | - Insert/delete columns using a SAI to define affected columns |
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| 90 | - ARB_EDIT4 |
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| 91 | - improved support for using multiple edit-windows |
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| 92 | - smoother refreshes |
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| 93 | - tweaked ORF display |
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| 94 | - tree importer/exporter |
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| 95 | - ARBs extended newick format (with bootstrap values) handled more restrictive now |
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| 96 | - fixed several bugs; improved errors/warnings |
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| 97 | - consensus trees |
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| 98 | - calculate from multiple existing trees (also allows to merge not completely overlapping trees) |
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| 99 | - fixed NJ-bootstrapping (no longer drops species) |
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| 100 | - tree display |
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| 101 | - Show brackets on open groups (dendrogram tree only) |
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| 102 | - rewrote IRS (folded) display |
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| 103 | - fixed tree key-bindings (mark, fold, ...) |
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| 104 | - improved several tree-commands (move, rotate, spread, length, width) |
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| 105 | - added a branch analysis tool |
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| 106 | - groups several functions previously availiable via menuitems (e.g. mark long branches, etc.) |
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| 107 | - added leaf-distance analysis |
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| 108 | - other tree functionality |
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| 109 | - treelist sortable now |
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| 110 | - new beautify-tree modes (radial tree / according to other tree) |
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| 111 | - function to remove marked/zombies from ALL trees |
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| 112 | - create multifurcations (by branchlength/bootstrap limit) |
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| 113 | - toggle 100% bootstrap values |
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| 114 | - tweaked printing (interface, overlapping) |
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| 115 | - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers |
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| 116 | - probe design: |
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| 117 | - added LOAD to result window |
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| 118 | - automation |
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| 119 | - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..) |
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| 120 | - arb_ntree can execute macro from command line |
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| 121 | - added "Never ask again" to modal question boxes (for better compatibility with macros) |
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| 122 | - a macro can be called for all marked species (once for each) |
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| 123 | - macros can be nested (i.e. can call other macros) |
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| 124 | - support for user-specific customization: |
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| 125 | - of GDE menus (in ~/.arb_prop/gde) |
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| 126 | - of import/export filters (in ~/.arb_prop/filter) |
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| 127 | - ACI (some new commands, bugfixes) |
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| 128 | - updated/added external tools: |
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| 129 | - added FastTree (version 2.1.7) |
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| 130 | - added MAFFT (version 7.055) |
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| 131 | - added MrBayes (version 3.2.1) |
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| 132 | - added MUSCLE (version 3.8.31) |
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| 133 | - added PHYML (2013/07/08; also kept old version 2.4.5) |
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| 134 | - added PROBCONS (version 1.12) |
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| 135 | - updated RAxML (version 7.7.2) |
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| 136 | - load/save for window specific settings (e.g. allows to share parts of configuration with other users) |
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| 137 | - Support for mouse-wheel |
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| 138 | - many unlisted bugfixes |
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| 139 | - many internal refactorings |
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| 140 | |
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| 141 | |
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| 142 | Fixes for arb_5.5 (15 Nov 2012): |
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| 143 | |
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| 144 | * arb_5.4 was broken (several external tools missing) |
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| 145 | |
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| 146 | |
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| 147 | Fixes for arb_5.4 (14 Nov 2012): |
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| 148 | |
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| 149 | * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000) |
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| 150 | * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling) |
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| 151 | * fixed several compilation issues (OSX; recent distro releases) |
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| 152 | |
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| 153 | |
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| 154 | Fixes for arb_5.3 (10 Nov 2011): |
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| 155 | |
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| 156 | - bugfixes |
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| 157 | - fixed wrong absolute/ecoli position reported for some designed probes |
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| 158 | - decompression error handling (pt-server build issues) |
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| 159 | - fixed 'codon_start' generated with wrong type |
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| 160 | - fixed a buffer overflow in ACI |
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| 161 | - report failures to write to /tmp |
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| 162 | - changes |
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| 163 | - markSpecies.pl: |
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| 164 | mark by accession number |
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| 165 | partial/ambiguous matches |
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| 166 | - internal fixes |
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| 167 | - compilation fixes for OSX |
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| 168 | - some patches for debian version (removed refs to xview, textedit, removed molphy(protml)) |
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| 169 | - removed obsolete dependency from libXp |
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| 170 | |
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| 171 | |
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| 172 | Fixes for arb_5.2 (5 Sep 2010): |
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| 173 | |
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| 174 | - bugfixes |
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| 175 | - quicksave did silently do nothing (especially not save anything) if an error occurred |
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| 176 | - ARB_EDIT4: crashed when using config with MANY unknown species |
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| 177 | - ARB_SECEDIT: crashed when trying to paint strand w/o any base |
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| 178 | - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo |
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| 179 | - changes |
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| 180 | - ARB uses xdg-open to display web-pages |
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| 181 | - internal fixes |
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| 182 | - karmic koala (gcc 4.4.1) |
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| 183 | - installation script |
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| 184 | - arb build process uses xsltproc instead of sablotron |
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| 185 | |
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| 186 | |
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| 187 | Fixes for arb_5.1 (1 Oct 2009): |
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| 188 | |
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| 189 | - fixed a bug in 'Create species from consensus' (created sequence was corrupted) |
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| 190 | - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction) |
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| 191 | - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell) |
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| 192 | - fixed broken demo.arb |
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| 193 | |
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| 194 | |
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| 195 | Major changes for arb_5.00 (4 Sep 2009): |
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| 196 | |
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| 197 | - ARB 64bit version |
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| 198 | - new genome importer |
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| 199 | - search for next relatives improved (normal search and fast-aligner) |
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| 200 | - new parameters to precise search |
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| 201 | - improved speed |
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| 202 | - partial sequence reach normal scores |
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| 203 | - search&query |
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| 204 | - supports regular expressions and ACI |
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| 205 | - track hit information |
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| 206 | - result sorting |
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| 207 | - Nameservers with add.field have to be started with default value |
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| 208 | You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat) |
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| 209 | - multiple PT-servers may be used in parallel |
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| 210 | - fixed multiprobe |
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| 211 | - type-conversion for DB fields |
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| 212 | - SILVA compatible import filters |
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| 213 | - Newick tree export: |
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| 214 | - optionally save in human-readable format (big) |
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| 215 | - closer to newick standard format (quoting style, comment, special chars in data) |
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| 216 | - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface) |
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| 217 | - Fixed sequence quality calculation |
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| 218 | - Secondary structures for proteins (DSSP) |
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| 219 | - Distance matrix (arb_dist): mark by distance to selected |
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| 220 | - ARB core |
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| 221 | - many bugfixes and improvements to reliability |
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| 222 | - faster sorting (general speedup) |
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| 223 | - improved sequence compression (avoid worse trees, better ratio) |
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| 224 | - improved handling of temporary files (permission/removal) |
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| 225 | - prints backtraces in userland |
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| 226 | - regular expression are POSIX standard now |
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| 227 | - macro record/playback |
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| 228 | - fixed several bugs |
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| 229 | - you need to re-record your old macros! |
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| 230 | - GUI: |
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| 231 | - disabled auto-focus, you need to click now |
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| 232 | - auto-raise windows on access |
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| 233 | - Minor things: |
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| 234 | - Ubuntu: packet installation for ARB |
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| 235 | - Fixed novice/expert mode |
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| 236 | - Mark deep/degenerated branches |
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| 237 | - Increased NDS entries |
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| 238 | - up-to-date Mac port (thx to Matt Cottrell) |
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| 239 | |
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| 240 | Major changes in ARB 07.12.07org (7 Dec 2007): |
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| 241 | |
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| 242 | - rewrote secondary structure editor |
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| 243 | - Sequence quality check |
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| 244 | - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc) |
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| 245 | - tweaked base frequency filter generation |
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| 246 | - Normal export (not using readseq) improved: |
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| 247 | - supports filters and gap removal |
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| 248 | - optimized for big amount of data |
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| 249 | - reworked export filters |
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| 250 | - Display translation with different ORFs in EDIT4 |
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| 251 | - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse. |
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| 252 | - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool) |
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| 253 | - more compact display in EDIT4 |
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| 254 | - capable to use iso10646 fonts |
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| 255 | - supports various gcc versions (2.95.3 - 4.1.1) |
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| 256 | - fixed a bug in DB optimization (occurred when fields had bigger protection than current) |
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| 257 | - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses |
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| 258 | different color for size-limited circles; fixed xfig-export-bug |
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| 259 | - Allows Branchlength <-> Bootstrap value transfer (lossy!) |
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| 260 | - fixed several scaling bugs in "folded tree"-mode |
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| 261 | - improved import-filter error-messages |
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| 262 | - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives |
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| 263 | several new possibilities: |
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| 264 | - export taxonomy via 'Export NDS list' |
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| 265 | - display taxonomy in Editor etc. |
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| 266 | - display of cascaded taxonomies |
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| 267 | - display taxonomy of tree_1 in tree_2 |
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| 268 | - allows to write taxonomy into database field of species |
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| 269 | - compare taxonomies of two trees |
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| 270 | - ... |
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| 271 | - ACI: |
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| 272 | - many new ACI commands |
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| 273 | - unified handling of binary ACI-operators |
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| 274 | - tracing of ACI actions for debugging purpose |
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| 275 | - ARB Neighbour joining: |
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| 276 | - bootstrap limit configurable |
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| 277 | - bugfix: when aborting bootstrap calculation, sometimes no tree was generated |
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| 278 | - EDIT4: |
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| 279 | - added unalign right (block-op) |
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| 280 | - added 'Save loaded properties' |
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| 281 | - GENE MAP: |
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| 282 | - multiple views possible at the same time |
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| 283 | - origin now at "12 o'clock" |
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| 284 | - implemented 'jump to gene' |
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| 285 | - tweaked file selection |
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| 286 | - Enhanced Search Depth for Probe Match --> max 20 MM |
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| 287 | - CLUSTALW: |
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| 288 | - separated menus for fast and slow alignment |
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| 289 | - most parameters accessible from inside ARB now |
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| 290 | - upgraded to PHYLIP 3.6 (adds PROML) |
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| 291 | - external programs may be called parallel (e.g. several treeing programs) |
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| 292 | - fixed bugs in protml and integration of protml |
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| 293 | - rewrote ASCII database import |
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| 294 | - arb_repair for databases of any size (script for database repair) |
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| 295 | - fixed bug in data compression |
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| 296 | - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse) |
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| 297 | - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000) |
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| 298 | - GDE menus cleanup |
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| 299 | - translation/re-alignment tweaked |
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| 300 | - unalign right (EDIT4) |
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| 301 | - visualization of SAIs in Probe Match Results |
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| 302 | - changed formatting of probe match results; increase # of allowed matches to 100.000; |
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| 303 | warn if results are truncated |
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| 304 | - PT server for genes |
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| 305 | - Probe design performance optimized |
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| 306 | - fixed NEXUS export format |
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| 307 | - exports group names into Newick format |
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| 308 | - import XML tree files |
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| 309 | - help for external tools now properly shown inside ARB |
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| 310 | |
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| 311 | Major changes in Beta 2003_08_22 (22 Aug 2003): |
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| 312 | |
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| 313 | - automatic formatting of alignments |
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| 314 | - SECEDIT may use EDIT4 colors |
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| 315 | - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!)) |
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| 316 | - updated clustalw to version 1.83 |
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| 317 | - Restore window sizes for ALL windows (too small sizes are ignored) |
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| 318 | - new algorithm to add partial sequences to an existing tree |
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| 319 | - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony |
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| 320 | - Top area of ARB_NTREE may be reduced to maximize display area |
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| 321 | - All arb menus may be detached (click dashed line at top of menu) |
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| 322 | - visualization of SAIs (as background color behind Sequences) |
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| 323 | - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties |
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| 324 | - PT-server occupies more memory => does less passes; more diagnostic output |
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| 325 | - small changes to status window (unhide behavior/time estimation) |
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| 326 | - menus and menu-hotkeys reorganized |
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| 327 | - colored buttons in color config windows |
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| 328 | - alignment concatenation (e.g. several different genes) |
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| 329 | - merging data of similar species (according selected database field) |
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| 330 | - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand) |
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| 331 | - expanded sellists |
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| 332 | - save/load fixed for multi probes |
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| 333 | - Binary SAIs are editable in ARB_EDIT4 |
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| 334 | - Information windows are detachable (allows to have multiple windows showing different items) |
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| 335 | - Scanning for hidden/unknown database fields improved and separated; |
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| 336 | possibility to remove unused fields. |
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| 337 | - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.) |
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| 338 | - updated fastDNAml to 1.2.2 |
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| 339 | - added AxML (accelerated fastDNAml 1.2.2) |
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| 340 | - Field transfer definitions for exporting gene-species |
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| 341 | - File Selection: - recursive search available |
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| 342 | - The ARB_NTREE macro recording/execution has been fixed |
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| 343 | - Colorize species (see demo.arb) |
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| 344 | - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display |
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| 345 | - 'IslandHopper' -- a new integrated aligner (beta) |
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| 346 | - Many improvements and bugfixes to secondary structure editor: |
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| 347 | - highlighting of search (i.e for probes) like in EDIT4 |
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| 348 | - interactive constraint editing (stretch/compress) |
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| 349 | - probe info |
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| 350 | - editing secondary structure in XFIG now possible |
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| 351 | - visualization of SAIs |
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| 352 | - import reads Unix, DOS, and MAC linefeeds |
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| 353 | - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help |
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| 354 | - tree and sequence export to XML ( DTDs are provided in ./lib/dtd ) |
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| 355 | (reloading of these XML files is planned for the future) |
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| 356 | - fixed problems with phylip-tree import/export (bootstrap values,comments,...) |
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| 357 | - search in all database fields possible ('[all fields]') |
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| 358 | - up to 10 quicksaves are kept |
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| 359 | - new ACI functions: upper, lower, caps, eval |
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| 360 | - variables for import filter programming |
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| 361 | - extract gene-species: creates acc; extraction to existing alignments |
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| 362 | - sequence of selected gene is mirrored in ARB_EDIT4/local_signature |
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| 363 | (=> selected gene can be highlighted in primary editor) |
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| 364 | - PCR primer-design for single genes |
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| 365 | - when selecting a gene, the corresponding gene-species is selected (if found) |
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| 366 | - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...) |
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| 367 | - file selection box in import window |
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| 368 | - mark item with double click works in all search&query windows |
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| 369 | - User masks: create new; 'edit enable' and 'marked' toggles (like in info window) |
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| 370 | - Fixed command line help for all Arb-modules |
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| 371 | - Fixed problem parsing fonts (should fix display problems with default fonts) |
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| 372 | - Mark mode now works in list-view as well (ARB_NTREE) |
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| 373 | - Fixed appearance of 'tiny little boxes' (everywhere) |
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| 374 | - Redesign of ARB help: |
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| 375 | - a HTML version is in $ARBHOME/lib/help_html |
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| 376 | - a text version is in $ARBHOME/lib/help (like before, but now generated) |
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| 377 | |
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| 378 | Major changes in Beta 2001_11_07 (7 Nov 2001): |
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| 379 | |
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| 380 | - design probes to maximum length of 60 nucleotides |
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| 381 | - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode) |
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| 382 | - import default changed to foreign data format, ali name '16s' |
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| 383 | - printing of multi-page-trees works again |
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| 384 | - implemented user defineable masks to access database fields |
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| 385 | - fixed bugs in pt-server (lockup, unknown species just after building pt-server) |
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| 386 | - improved performance during pt-server-build |
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| 387 | - several programs coming along with ARB where updated (PHYLIP,...) |
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| 388 | - reads EMBL genom files |
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| 389 | - support for experiments (genom databases only) |
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| 390 | |
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| 391 | Major changes in Beta 2001_07_24 (24 Jul 2001): |
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| 392 | |
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| 393 | - basic support for genoms (Gene Map, reads Genebank files) |
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| 394 | - ported to libc6 |
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