| 1 | ARB change log |
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| 2 | |
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| 3 | Ticket references |
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| 4 | |
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| 5 | Referenced ticket numbers are linked when you view this information |
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| 6 | at http://help.arb-home.de/changes.html |
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| 7 | |
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| 8 | Major changes for next release: |
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| 9 | |
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| 10 | - split alignments (#846) |
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| 11 | - detect poorly aligned helical regions in editor (#854) |
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| 12 | - tweaked 'Helix settings' in EDIT4 |
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| 13 | - defaults changed for GG ('#'->'='), TT + UU ('+'->'#'), ambiguity codes (''->'%') |
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| 14 | - added several predefined configs (traditional, two handling ambiguity codes) |
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| 15 | - display in SECEDIT updates after helix changes |
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| 16 | - tweaked 'Track alignment changes' |
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| 17 | - automatically adds generated fields to species info. |
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| 18 | - enhanced documentation (recommended workflow) |
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| 19 | - tweaked progress |
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| 20 | - better estimation for NJ, ConsensusTree, matrix calculation + PVP |
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| 21 | - uses weighted progresses (#789) |
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| 22 | - also fixes progress overflow (#807) |
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| 23 | - support for longer periods (weeks, months, ...) |
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| 24 | - prefer overestimation |
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| 25 | - log to console (estimates finish) |
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| 26 | - include SINA (1.7.2 patched) |
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| 27 | - interface auto-adapts to sina version (still compatible with 1.3; currently needs patched version for 1.7.2) |
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| 28 | - added script arb_sina_install_from_fat_tarball.sh (allows to install sina from fat-tarballs provided via arb homepage) |
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| 29 | - improved macro scriptability |
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| 30 | - now synchronizes external tools (#869) |
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| 31 | - properly allows quitting arb (#867) |
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| 32 | - allow to plan user interaction (#856) |
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| 33 | - append output from external tools to arb logfile. |
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| 34 | - FastTree |
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| 35 | - added support for protein sequences. |
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| 36 | - customizable from GUI (rate categories, NJ, bootstraps). |
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| 37 | - upgraded to version 2.1.11 |
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| 38 | - arb now provides single+multi processor versions of FastTree |
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| 39 | - NDS (Node display setup; #841) |
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| 40 | - specifying a zero WIDTH now means "unlimited" (backward compatible). |
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| 41 | - avoid unwanted truncation (NDS-export, saved distance matrix). |
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| 42 | - tree/export (using NDS) |
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| 43 | - no longer truncates labels. |
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| 44 | - group-labels are generated by NDS now. |
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| 45 | - raise an error if non-ASCII characters are used in label (optionally). |
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| 46 | - import from calcsheet: |
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| 47 | - support for fuzzy matches (#865) |
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| 48 | - can handle empty trailing cells |
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| 49 | - added SAVE button to arb message window (saves pos+size+content) |
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| 50 | - minor changes: |
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| 51 | - 'Mark/Unmark listed' buttons in search window |
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| 52 | - new ACI command 'dupidx' supporting group enumeration (#863) |
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| 53 | - added |
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| 54 | - script to analyze database structure (#866; generated reports allow database comparison) |
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| 55 | - macros to cleanup database ("keep_listed_(trees|SAIs|speciesSelections).amc") |
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| 56 | - documentation (arb integrated help): |
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| 57 | - length checked + corrected for preformatted text and titles |
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| 58 | - minor layout changes |
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| 59 | - link tickets and URLs (html) |
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| 60 | |
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| 61 | Fixes for arb-7.0.1 (31 Jan 2022): |
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| 62 | |
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| 63 | - fix perl compatibility for macOS 12 |
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| 64 | |
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| 65 | Major changes for arb-7.0 (1 Sep 2021): |
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| 66 | |
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| 67 | - ARB PARSIMONY |
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| 68 | * topology optimization |
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| 69 | - now (by default) strictly restricted to marked/visible parts of the tree (#640) |
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| 70 | - restriction now customizable (marked/all; visible/all) |
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| 71 | - tree costs for protein-data were not independent from root-position (as expected by model; #633). |
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| 72 | Caused infinite running optimization under some circumstances. |
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| 73 | - optimize-modes now strictly restrict to clicked subtrees. single/repeated optimization possible. |
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| 74 | - KL-optimizer |
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| 75 | * static path reduction slightly changed meaning. changed default settings. |
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| 76 | * removed randomness (was just covering some bugs) |
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| 77 | * improved general optimization speed |
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| 78 | * branchlength calculation |
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| 79 | - "forgot" to recalculate lengths under some conditions. fixed. |
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| 80 | - is now independent of tree-root position (#641) |
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| 81 | * adding species |
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| 82 | - 'add partial species' failed if two partial species had NO overlap (#609). fixed. |
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| 83 | - in 'add species + NNI' local optimization quality depended on insert position. fixed. |
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| 84 | - insertion of multiple species is now done independently (=unordered; #643) |
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| 85 | - performance improved (esp. for many added species/big trees; #643) |
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| 86 | * generally improved combine performance (using SSE) |
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| 87 | * generally reduced the number of performed combines (skipping many useless) |
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| 88 | * added function to randomize (parts of) the tree |
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| 89 | * warns about insufficient sequence data (e.g. as result of too restrictive filtering; #631) |
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| 90 | * fixed 'RESTORE' (crashed after deleting species from tree; #528) |
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| 91 | * corrected handling of dots ('.') while combining ancestor sequences |
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| 92 | * fixed a bunch of internal bugs (#620, #627, #645, ...) |
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| 93 | * added species-info mode |
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| 94 | - added missing translation tables (genetic codes 24-31) |
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| 95 | - added amino acid code Xle(=J), which means Ile(=I) or Leu(=L) |
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| 96 | - DNA realigner |
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| 97 | * several unjustified failures will no longer happen (fixes #419 and most likely #145) |
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| 98 | - correctly re-syncs after 'X' (if possible at all) |
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| 99 | - no longer fails for 'B', 'J' and 'Z' |
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| 100 | - accepts 3 or more consecutive IUPAC codes in DNA |
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| 101 | * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed) |
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| 102 | * fixed several minor bugs (#563,..) |
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| 103 | - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO) |
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| 104 | - species selections (editor configurations): |
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| 105 | * visualisation of multiple selections in standard tree view (#658; example in database demo.arb) |
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| 106 | * order can be changed; each configuration has a comment |
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| 107 | - import/export (species,sequence): |
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| 108 | * manage/edit/test import-/export-filter-definitions from inside ARB (#691) |
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| 109 | * import can store configuration of imported species (#607) |
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| 110 | * field transfer sets (#562) may be used to customize import/export behavior (also usable from arb merge-tool) |
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| 111 | * corrected EMBL export filter (numbers at seq.data; #638) |
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| 112 | * detected duplicates no longer abort complete import (#779) |
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| 113 | * new CLI sequence exporter 'arb_export_seq_filtered' (#743) |
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| 114 | - Tree shading (#443) |
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| 115 | * according to values stored in database |
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| 116 | * according to given topology (useful when comparing topologies) |
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| 117 | * added customisable color ranges (#682) |
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| 118 | - support for extra database compression (using gzip, bzip2, xz; #665); databases cannot be opened by versions before arb-7.0 |
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| 119 | - ARB_EDIT4: |
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| 120 | * display selected database fields as flags (allowing to toggle their value; #261). |
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| 121 | Example use: easily mark sequence as "curated" after manually checking its alignment. |
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| 122 | * allow to load missing SAIs |
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| 123 | * "view differences" to a reference sequence: |
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| 124 | - customizable: |
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| 125 | * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence) |
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| 126 | * case-sensitivity |
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| 127 | * ignore different gap-types |
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| 128 | - equal data also gets hidden in consensus |
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| 129 | - refresh differences of all displayed sequences, when data of selected sequences changes |
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| 130 | - change reference sequence using CTRL-R or automatically let it follow the cursor |
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| 131 | - added hotkey to toggle mode: CTRL-D |
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| 132 | - fixed minor bugs |
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| 133 | * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI |
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| 134 | - now both calculations are strictly consistent (#663): |
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| 135 | * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes |
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| 136 | * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus) |
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| 137 | - added sliders to consensus definition windows |
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| 138 | - user defined consensus settings exchangable between both consensus setups |
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| 139 | - fixed and updated documentation |
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| 140 | * added species-info mode + database save (#52,#362) |
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| 141 | * predefined SAI color translation for PVP |
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| 142 | - changes to SAI generation |
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| 143 | * MAX_FREQUENCY: |
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| 144 | - considers IUPAC ambiguity codes proportionally |
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| 145 | - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%) |
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| 146 | * POS_VAR_BY_PARSIMONY (PVP): |
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| 147 | - now (again) works with amino acid data (#782) |
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| 148 | - added CLI tool 'arb_calc_pvp' (#701) |
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| 149 | * implemented a SAI calculator (allows to modify or combine multiple SAIs) |
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| 150 | - expand zombies in tree (unfold groups; #22) |
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| 151 | - compare taxonomy (and mark differences; #651) |
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| 152 | - search&query for taxonomic groups (#652) |
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| 153 | - many search criteria (name, size, marked, nesting-level, ingroup-distance (#653), ...) |
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| 154 | - search multiple trees, detect duplicate and missing groups |
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| 155 | - operations on found groups (delete, rename, fold, mark) |
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| 156 | - added concept of "inverse groups" (aka "keeled groups"; #735) |
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| 157 | - group transfer between trees (#780): |
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| 158 | - penalties can be customized in detail |
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| 159 | - quality reports (to log and optionally to target name) |
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| 160 | - synchronize positions of roots of multiple trees (#449) |
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| 161 | - external (command line) aligners (#504): |
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| 162 | * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type |
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| 163 | * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment |
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| 164 | * no longer ask what to do with aligned sequence, just overwrite it |
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| 165 | - only warn about real sequence changes (so please do NOT ignore from now on!) |
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| 166 | - config-managers: |
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| 167 | * possibility to restore factory defaults |
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| 168 | * added comment field for configurations |
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| 169 | * added them throughout arb (#647) |
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| 170 | - added slide controls throughout arb (#656) |
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| 171 | - tree (display) options: |
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| 172 | * fine grained scaling |
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| 173 | * group display (shading, customizable counters (#118,#209), triangle clades, name display position) |
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| 174 | * bootstrap values (filter by upper/lower limits, display position/styles, on/off toggle; #614) |
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| 175 | * diagonal branch style (#578) |
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| 176 | * parent branch position |
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| 177 | * all options are now also supported by ARB_PARSIMONY |
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| 178 | * improved auto-jump; now also works for groups |
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| 179 | * added optional auto-unfolding (to selected group/species) |
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| 180 | * select group on fold/unfold/create/move/.. |
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| 181 | * draw selected group in cursor-color (#709) |
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| 182 | * added keys for tree-traversal (moving to selected species or group; #687) |
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| 183 | - synchronized tree scrolling (#683) |
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| 184 | - colorsets were invalidated by generating new IDs (#660). fixed. |
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| 185 | - added alternate RAxML (DNA only; version 8.2.8) |
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| 186 | - multicore support (automatically activates recommended number of threads) |
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| 187 | - evaluation, optimization and extension of existing trees with RAxML (#681) |
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| 188 | - fix performance of |
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| 189 | * "format sequences" (broken in arb-6.0.x series; #702) |
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| 190 | * nameserver for huge databases (#646) |
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| 191 | * closing arb (if database uses fastload file; #649) |
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| 192 | - ACI |
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| 193 | - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands |
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| 194 | - allow access to other species via ID or accession number (findspec, ...) |
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| 195 | - improved ACI debugging: more verbose tracing (console log accessible from inside ARB) |
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| 196 | - NDS optionally uses only visible definitions |
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| 197 | - Search&Query: |
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| 198 | * sort results numerically (#203) |
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| 199 | * recursive search through all fields (#773) |
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| 200 | - Species information window: improved detachment, field selection (#695) |
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| 201 | - improved macro compatibility: |
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| 202 | * check compatibility with installed perl version during arb startup (#754) |
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| 203 | * esp. tweaked compatibility of 'Search&Query' and 'Species information window' |
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| 204 | * fixed a lot of internal names (missing or duplicated) which are used for macros (#429) |
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| 205 | - improved OSX compatibility (thx to Jan Gerken) |
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| 206 | - updated integrated documentation (#409) |
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| 207 | |
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| 208 | |
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| 209 | Fixes for arb-6.0.6 (22 Aug 2016): |
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| 210 | |
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| 211 | - fixes for gcc 6.1.0 |
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| 212 | - tested gcc 4.9.4 + 5.4.0 |
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| 213 | |
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| 214 | Fixes for arb-6.0.5 (4 May 2016): |
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| 215 | |
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| 216 | - fixes for ubuntu 16.04 build |
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| 217 | |
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| 218 | Fixes for arb-6.0.4 (2 May 2016): |
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| 219 | |
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| 220 | - fixes for OSX build (SIP, accepted compilers) |
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| 221 | |
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| 222 | Fixes for arb-6.0.3 (19 Nov 2015): |
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| 223 | |
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| 224 | - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch) |
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| 225 | |
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| 226 | Fixes for arb-6.0.2 (8 Aug 2014): |
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| 227 | |
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| 228 | - compile issues on Snow Leopard (OSX 10.6) |
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| 229 | - merge Debian security fix for CVE-2008-5378 |
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| 230 | - small changes to build system for Debian |
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| 231 | - add desktop integration files |
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| 232 | |
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| 233 | Fixes for arb-6.0.1 (22 Jul 2014): |
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| 234 | |
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| 235 | - arb_parsimony |
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| 236 | - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group) |
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| 237 | - corrected branchlength calculation for "Add marked partial species" |
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| 238 | - dots were treated as gaps for protein sequences (now treated as 'X'; analog to DNA treating gaps as 'N'; #144). thx to Yan Shi for detecting that problem! |
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| 239 | - print |
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| 240 | - preview failed (showed empty postscript file) |
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| 241 | - print to file now always saves in user home |
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| 242 | - raxml (import tree with bootstrap values) |
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| 243 | |
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| 244 | Major changes for arb-6.0 (4 Jun 2014): |
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| 245 | |
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| 246 | - merge databases allows to |
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| 247 | - merge from an existing database into the database loaded in ARB_NT |
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| 248 | - merge to existing databases from the database loaded in ARB_NT |
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| 249 | - ARB can now |
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| 250 | - be restarted with another database and |
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| 251 | - a second instance of ARB can be opened |
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| 252 | - ARB_DIST |
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| 253 | - Detect clusters of species with similar sequences (OTUs) |
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| 254 | - allow automatic recalculation of matrix and/or tree whenever some parameter or |
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| 255 | data changes (only makes sense for smaller species sets) |
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| 256 | - extract distance matrix from tree |
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| 257 | - Rewrote chimera check. Allows filtering |
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| 258 | - added RNACMA (computes clusters of correlated positions) |
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| 259 | - PT-Server |
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| 260 | - changed behavior |
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| 261 | - 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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| 262 | - reports previously missing hits in joined genes |
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| 263 | - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible |
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| 264 | matches that go beyond the end of the sequence) |
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| 265 | - dots in the middle of the alignment act like the sequence ends there |
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| 266 | - minimum probe length reduced to 2 (was 6) |
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| 267 | - allow up to 50% of probe to mismatch |
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| 268 | - performance |
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| 269 | - optimized memory-estimation (will build in fewer passes) |
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| 270 | - uses any number of passes (not only 1, 5, 25, ...) |
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| 271 | - allows to define used memory by setting environment variable ARB_MEMORY |
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| 272 | - reduced memory needed to build/run ptserver (approx. 50%) |
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| 273 | - reduced size of indexfile (.pt) to ~50% |
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| 274 | - fast startup of existing ptservers |
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| 275 | - probe design |
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| 276 | - faster in many cases |
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| 277 | - allow to design probes of length 8 (previously 10) |
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| 278 | - allow to design probes with different lengths (specifying min/max length) |
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| 279 | - fixed number of outgroup hits reported when decreasing temperature |
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| 280 | (now each outgroup member only occurs once) |
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| 281 | - show possible reasons why no probes could be designed |
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| 282 | - probe match (allow any number of mismatches) |
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| 283 | - next relative search |
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| 284 | - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences) |
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| 285 | - corrected and improved scaling of relative scores |
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| 286 | - more accurate scores (due to fixes in PT-Server; see below) |
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| 287 | - faster in many cases |
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| 288 | - show errors from ptserver build in ARB |
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| 289 | - fast-aligner |
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| 290 | - searches next-relatives based on selected column-block |
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| 291 | - align multiple column-blocks based on SAI |
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| 292 | - Rewrote alignment adaption during merge |
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| 293 | - Insert/delete columns using a SAI to define affected columns |
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| 294 | - ARB_EDIT4 |
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| 295 | - improved support for using multiple edit-windows |
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| 296 | - smoother refreshes |
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| 297 | - tweaked ORF display |
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| 298 | - tree importer/exporter |
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| 299 | - ARBs extended newick format (with bootstrap values) handled more restrictive now |
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| 300 | - fixed several bugs; improved errors/warnings |
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| 301 | - consensus trees |
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| 302 | - calculate from multiple existing trees (also allows to merge not completely overlapping trees) |
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| 303 | - fixed NJ-bootstrapping (no longer drops species) |
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| 304 | - tree display |
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| 305 | - Show brackets on open groups (dendrogram tree only) |
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| 306 | - rewrote IRS (folded) display |
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| 307 | - fixed tree key-bindings (mark, fold, ...) |
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| 308 | - improved several tree-commands (move, rotate, spread, length, width) |
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| 309 | - added a branch analysis tool |
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| 310 | - groups several functions previously available via menuitems (e.g. mark long branches, etc.) |
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| 311 | - added leaf-distance analysis |
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| 312 | - other tree functionality |
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| 313 | - treelist sortable now |
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| 314 | - new beautify-tree modes (radial tree / according to other tree) |
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| 315 | - function to remove marked/zombies from ALL trees |
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| 316 | - create multifurcations (by branchlength/bootstrap limit) |
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| 317 | - toggle 100% bootstrap values |
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| 318 | - tweaked printing (interface, overlapping) |
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| 319 | - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers |
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| 320 | - probe design: |
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| 321 | - added LOAD to result window |
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| 322 | - automation |
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| 323 | - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..) |
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| 324 | - arb_ntree can execute macro from command line |
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| 325 | - added "Never ask again" to modal question boxes (for better compatibility with macros) |
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| 326 | - a macro can be called for all marked species (once for each) |
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| 327 | - macros can be nested (i.e. can call other macros) |
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| 328 | - support for user-specific customization: |
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| 329 | - of GDE menus (in ~/.arb_prop/gde) |
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| 330 | - of import/export filters (in ~/.arb_prop/filter) |
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| 331 | - ACI (some new commands, bugfixes) |
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| 332 | - updated/added external tools: |
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| 333 | - added FastTree (version 2.1.7) |
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| 334 | - added MAFFT (version 7.055) |
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| 335 | - added MrBayes (version 3.2.1) |
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| 336 | - added MUSCLE (version 3.8.31) |
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| 337 | - added PHYML (2013/07/08; also kept old version 2.4.5) |
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| 338 | - added PROBCONS (version 1.12) |
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| 339 | - updated RAxML (version 7.7.2) |
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| 340 | - load/save for window specific settings (e.g. allows to share parts of configuration with other users) |
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| 341 | - Support for mouse-wheel |
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| 342 | - many unlisted bugfixes |
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| 343 | - many internal refactorings |
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| 344 | |
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| 345 | |
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| 346 | Fixes for arb_5.5 (15 Nov 2012): |
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| 347 | |
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| 348 | * arb_5.4 was broken (several external tools missing) |
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| 349 | |
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| 350 | |
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| 351 | Fixes for arb_5.4 (14 Nov 2012): |
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| 352 | |
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| 353 | * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000) |
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| 354 | * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling) |
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| 355 | * fixed several compilation issues (OSX; recent distro releases) |
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| 356 | |
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| 357 | |
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| 358 | Fixes for arb_5.3 (10 Nov 2011): |
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| 359 | |
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| 360 | - bugfixes |
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| 361 | - fixed wrong absolute/ecoli position reported for some designed probes |
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| 362 | - decompression error handling (pt-server build issues) |
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| 363 | - fixed 'codon_start' generated with wrong type |
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| 364 | - fixed a buffer overflow in ACI |
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| 365 | - report failures to write to /tmp |
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| 366 | - changes |
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| 367 | - markSpecies.pl: |
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| 368 | mark by accession number |
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| 369 | partial/ambiguous matches |
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| 370 | - internal fixes |
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| 371 | - compilation fixes for OSX |
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| 372 | - some patches for debian version (removed refs to xview, textedit, removed molphy(protml)) |
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| 373 | - removed obsolete dependency from libXp |
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| 374 | |
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| 375 | |
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| 376 | Fixes for arb_5.2 (5 Sep 2010): |
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| 377 | |
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| 378 | - bugfixes |
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| 379 | - quicksave did silently do nothing (especially not save anything) if an error occurred |
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| 380 | - ARB_EDIT4: crashed when using config with MANY unknown species |
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| 381 | - ARB_SECEDIT: crashed when trying to paint strand w/o any base |
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| 382 | - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo |
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| 383 | - changes |
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| 384 | - ARB uses xdg-open to display web-pages |
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| 385 | - internal fixes |
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| 386 | - karmic koala (gcc 4.4.1) |
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| 387 | - installation script |
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| 388 | - arb build process uses xsltproc instead of sablotron |
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| 389 | |
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| 390 | |
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| 391 | Fixes for arb_5.1 (1 Oct 2009): |
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| 392 | |
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| 393 | - fixed a bug in 'Create species from consensus' (created sequence was corrupted) |
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| 394 | - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction) |
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| 395 | - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell) |
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| 396 | - fixed broken demo.arb |
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| 397 | |
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| 398 | |
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| 399 | Major changes for arb_5.00 (4 Sep 2009): |
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| 400 | |
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| 401 | - ARB 64bit version |
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| 402 | - new genome importer |
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| 403 | - search for next relatives improved (normal search and fast-aligner) |
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| 404 | - new parameters to precise search |
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| 405 | - improved speed |
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| 406 | - partial sequence reach normal scores |
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| 407 | - search&query |
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| 408 | - supports regular expressions and ACI |
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| 409 | - track hit information |
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| 410 | - result sorting |
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| 411 | - Nameservers with add.field have to be started with default value |
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| 412 | You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat) |
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| 413 | - multiple PT-servers may be used in parallel |
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| 414 | - fixed multiprobe |
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| 415 | - type-conversion for DB fields |
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| 416 | - SILVA compatible import filters |
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| 417 | - Newick tree export: |
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| 418 | - optionally save in human-readable format (big) |
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| 419 | - closer to newick standard format (quoting style, comment, special chars in data) |
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| 420 | - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface) |
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| 421 | - Fixed sequence quality calculation |
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| 422 | - Secondary structures for proteins (DSSP) |
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| 423 | - Distance matrix (arb_dist): mark by distance to selected |
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| 424 | - ARB core |
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| 425 | - many bugfixes and improvements to reliability |
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| 426 | - faster sorting (general speedup) |
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| 427 | - improved sequence compression (avoid worse trees, better ratio) |
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| 428 | - improved handling of temporary files (permission/removal) |
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| 429 | - prints backtraces in userland |
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| 430 | - regular expression are POSIX standard now |
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| 431 | - macro record/playback |
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| 432 | - fixed several bugs |
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| 433 | - you need to re-record your old macros! |
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| 434 | - GUI: |
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| 435 | - disabled auto-focus, you need to click now |
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| 436 | - auto-raise windows on access |
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| 437 | - Minor things: |
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| 438 | - Ubuntu: packet installation for ARB |
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| 439 | - Fixed novice/expert mode |
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| 440 | - Mark deep/degenerated branches |
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| 441 | - Increased NDS entries |
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| 442 | - up-to-date Mac port (thx to Matt Cottrell) |
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| 443 | |
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| 444 | Major changes in ARB 07.12.07org (7 Dec 2007): |
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| 445 | |
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| 446 | - rewrote secondary structure editor |
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| 447 | - Sequence quality check |
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| 448 | - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc) |
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| 449 | - tweaked base frequency filter generation |
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| 450 | - Normal export (not using readseq) improved: |
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| 451 | - supports filters and gap removal |
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| 452 | - optimized for big amount of data |
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| 453 | - reworked export filters |
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| 454 | - Display translation with different ORFs in EDIT4 |
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| 455 | - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse. |
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| 456 | - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool) |
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| 457 | - more compact display in EDIT4 |
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| 458 | - capable to use iso10646 fonts |
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| 459 | - supports various gcc versions (2.95.3 - 4.1.1) |
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| 460 | - fixed a bug in DB optimization (occurred when fields had bigger protection than current) |
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| 461 | - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses |
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| 462 | different color for size-limited circles; fixed xfig-export-bug |
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| 463 | - Allows Branchlength <-> Bootstrap value transfer (lossy!) |
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| 464 | - fixed several scaling bugs in "folded tree"-mode |
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| 465 | - improved import-filter error-messages |
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| 466 | - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives |
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| 467 | several new possibilities: |
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| 468 | - export taxonomy via 'Export NDS list' |
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| 469 | - display taxonomy in Editor etc. |
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| 470 | - display of cascaded taxonomies |
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| 471 | - display taxonomy of tree_1 in tree_2 |
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| 472 | - allows to write taxonomy into database field of species |
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| 473 | - compare taxonomies of two trees |
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| 474 | - ... |
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| 475 | - ACI: |
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| 476 | - many new ACI commands |
|---|
| 477 | - unified handling of binary ACI-operators |
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| 478 | - tracing of ACI actions for debugging purpose |
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| 479 | - ARB Neighbour joining: |
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| 480 | - bootstrap limit configurable |
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| 481 | - bugfix: when aborting bootstrap calculation, sometimes no tree was generated |
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| 482 | - EDIT4: |
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| 483 | - added unalign right (block-op) |
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| 484 | - added 'Save loaded properties' |
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| 485 | - GENE MAP: |
|---|
| 486 | - multiple views possible at the same time |
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| 487 | - origin now at "12 o'clock" |
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| 488 | - implemented 'jump to gene' |
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| 489 | - tweaked file selection |
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| 490 | - Enhanced Search Depth for Probe Match --> max 20 MM |
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| 491 | - CLUSTALW: |
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| 492 | - separated menus for fast and slow alignment |
|---|
| 493 | - most parameters accessible from inside ARB now |
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| 494 | - upgraded to PHYLIP 3.6 (adds PROML) |
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| 495 | - external programs may be called parallel (e.g. several treeing programs) |
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| 496 | - fixed bugs in protml and integration of protml |
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| 497 | - rewrote ASCII database import |
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| 498 | - arb_repair for databases of any size (script for database repair) |
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| 499 | - fixed bug in data compression |
|---|
| 500 | - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse) |
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| 501 | - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000) |
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| 502 | - GDE menus cleanup |
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| 503 | - translation/re-alignment tweaked |
|---|
| 504 | - unalign right (EDIT4) |
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| 505 | - visualization of SAIs in Probe Match Results |
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| 506 | - changed formatting of probe match results; increase # of allowed matches to 100.000; |
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| 507 | warn if results are truncated |
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| 508 | - PT server for genes |
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| 509 | - Probe design performance optimized |
|---|
| 510 | - fixed NEXUS export format |
|---|
| 511 | - exports group names into Newick format |
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| 512 | - import XML tree files |
|---|
| 513 | - help for external tools now properly shown inside ARB |
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| 514 | |
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| 515 | Major changes in Beta 2003_08_22 (22 Aug 2003): |
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| 516 | |
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| 517 | - automatic formatting of alignments |
|---|
| 518 | - SECEDIT may use EDIT4 colors |
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| 519 | - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!)) |
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| 520 | - updated clustalw to version 1.83 |
|---|
| 521 | - Restore window sizes for ALL windows (too small sizes are ignored) |
|---|
| 522 | - new algorithm to add partial sequences to an existing tree |
|---|
| 523 | - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony |
|---|
| 524 | - Top area of ARB_NTREE may be reduced to maximize display area |
|---|
| 525 | - All arb menus may be detached (click dashed line at top of menu) |
|---|
| 526 | - visualization of SAIs (as background color behind Sequences) |
|---|
| 527 | - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties |
|---|
| 528 | - PT-server occupies more memory => does less passes; more diagnostic output |
|---|
| 529 | - small changes to status window (unhide behavior/time estimation) |
|---|
| 530 | - menus and menu-hotkeys reorganized |
|---|
| 531 | - colored buttons in color config windows |
|---|
| 532 | - alignment concatenation (e.g. several different genes) |
|---|
| 533 | - merging data of similar species (according selected database field) |
|---|
| 534 | - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand) |
|---|
| 535 | - expanded sellists |
|---|
| 536 | - save/load fixed for multi probes |
|---|
| 537 | - Binary SAIs are editable in ARB_EDIT4 |
|---|
| 538 | - Information windows are detachable (allows to have multiple windows showing different items) |
|---|
| 539 | - Scanning for hidden/unknown database fields improved and separated; |
|---|
| 540 | possibility to remove unused fields. |
|---|
| 541 | - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.) |
|---|
| 542 | - updated fastDNAml to 1.2.2 |
|---|
| 543 | - added AxML (accelerated fastDNAml 1.2.2) |
|---|
| 544 | - Field transfer definitions for exporting gene-species |
|---|
| 545 | - File Selection: - recursive search available |
|---|
| 546 | - The ARB_NTREE macro recording/execution has been fixed |
|---|
| 547 | - Colorize species (see demo.arb) |
|---|
| 548 | - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display |
|---|
| 549 | - 'IslandHopper' -- a new integrated aligner (beta) |
|---|
| 550 | - Many improvements and bugfixes to secondary structure editor: |
|---|
| 551 | - highlighting of search (i.e for probes) like in EDIT4 |
|---|
| 552 | - interactive constraint editing (stretch/compress) |
|---|
| 553 | - probe info |
|---|
| 554 | - editing secondary structure in XFIG now possible |
|---|
| 555 | - visualization of SAIs |
|---|
| 556 | - import reads Unix, DOS, and MAC linefeeds |
|---|
| 557 | - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help |
|---|
| 558 | - tree and sequence export to XML ( DTDs are provided in ./lib/dtd ) |
|---|
| 559 | (reloading of these XML files is planned for the future) |
|---|
| 560 | - fixed problems with phylip-tree import/export (bootstrap values,comments,...) |
|---|
| 561 | - search in all database fields possible ('[all fields]') |
|---|
| 562 | - up to 10 quicksaves are kept |
|---|
| 563 | - new ACI functions: upper, lower, caps, eval |
|---|
| 564 | - variables for import filter programming |
|---|
| 565 | - extract gene-species: creates acc; extraction to existing alignments |
|---|
| 566 | - sequence of selected gene is mirrored in ARB_EDIT4/local_signature |
|---|
| 567 | (=> selected gene can be highlighted in primary editor) |
|---|
| 568 | - PCR primer-design for single genes |
|---|
| 569 | - when selecting a gene, the corresponding gene-species is selected (if found) |
|---|
| 570 | - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...) |
|---|
| 571 | - file selection box in import window |
|---|
| 572 | - mark item with double click works in all search&query windows |
|---|
| 573 | - User masks: create new; 'edit enable' and 'marked' toggles (like in info window) |
|---|
| 574 | - Fixed command line help for all Arb-modules |
|---|
| 575 | - Fixed problem parsing fonts (should fix display problems with default fonts) |
|---|
| 576 | - Mark mode now works in list-view as well (ARB_NTREE) |
|---|
| 577 | - Fixed appearance of 'tiny little boxes' (everywhere) |
|---|
| 578 | - Redesign of ARB help: |
|---|
| 579 | - a HTML version is in $ARBHOME/lib/help_html |
|---|
| 580 | - a text version is in $ARBHOME/lib/help (like before, but now generated) |
|---|
| 581 | |
|---|
| 582 | Major changes in Beta 2001_11_07 (7 Nov 2001): |
|---|
| 583 | |
|---|
| 584 | - design probes to maximum length of 60 nucleotides |
|---|
| 585 | - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode) |
|---|
| 586 | - import default changed to foreign data format, ali name '16s' |
|---|
| 587 | - printing of multi-page-trees works again |
|---|
| 588 | - implemented user defineable masks to access database fields |
|---|
| 589 | - fixed bugs in pt-server (lockup, unknown species just after building pt-server) |
|---|
| 590 | - improved performance during pt-server-build |
|---|
| 591 | - several programs coming along with ARB where updated (PHYLIP,...) |
|---|
| 592 | - reads EMBL genom files |
|---|
| 593 | - support for experiments (genom databases only) |
|---|
| 594 | |
|---|
| 595 | Major changes in Beta 2001_07_24 (24 Jul 2001): |
|---|
| 596 | |
|---|
| 597 | - basic support for genoms (Gene Map, reads Genebank files) |
|---|
| 598 | - ported to libc6 |
|---|
| 599 | |
|---|
| 600 | Changes in ancient versions (last century): |
|---|
| 601 | |
|---|
| 602 | - see http://help.arb-home.de/version.html |
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