1 | ARB change log |
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2 | |
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3 | |
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4 | Fixes for arb_5.1: |
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5 | |
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6 | * fixed a bug in 'Create species from consensus' (created sequence was corrupted) |
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7 | * fixed 2 bugs in optimize DB (alignment w/o data, missing transaction) |
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8 | * updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell) |
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9 | * fixed broken demo.arb |
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10 | |
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11 | |
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12 | Major changes for arb_5.00: |
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13 | |
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14 | - ARB 64bit version |
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15 | - new genome importer |
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16 | - search for next relatives improved (normal search and fast-aligner) |
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17 | * new parameters to precise search |
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18 | * improved speed |
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19 | * partial sequence reach normal scores |
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20 | - search&query |
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21 | * supports regular expressions and ACI |
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22 | * track hit information |
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23 | * result sorting |
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24 | - Nameservers with add.field have to be started with default value |
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25 | You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat) |
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26 | - multiple PT-servers may be used in parallel |
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27 | - fixed multiprobe |
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28 | - type-conversion for DB fields |
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29 | - SILVA compatible import filters |
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30 | - Newick tree export: |
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31 | * optionally save in human-readable format (big) |
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32 | * closer to newick standard format (quoting style, comment, special chars in data) |
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33 | - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface) |
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34 | - Fixed sequence quality calculation |
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35 | - Secondary structures for proteins (DSSP) |
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36 | - Distance matrix (arb_dist): mark by distance to selected |
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37 | - ARB core |
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38 | * many bugfixes and improvements to reliability |
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39 | * faster sorting (general speedup) |
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40 | * improved sequence compression (avoid worse trees, better ratio) |
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41 | * improved handling of temporary files (permission/removal) |
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42 | * prints backtraces in userland |
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43 | * regular expression are POSIX standard now |
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44 | - macro record/playback |
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45 | * fixed several bugs |
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46 | * you need to re-record your old macros! |
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47 | - GUI: |
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48 | * disabled auto-focus, you need to click now |
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49 | * auto-raise windows on access |
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50 | - Minor things: |
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51 | * Ubuntu: packet installation for ARB |
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52 | * Fixed novice/expert mode |
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53 | * Mark deep/degenerated branches |
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54 | * Increased NDS entries |
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55 | - up-to-date Mac port (thx to Matt Cottrell) |
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56 | |
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57 | Major changes in ARB 07.12.07org: |
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58 | |
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59 | - rewrote secondary structure editor |
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60 | - Sequence quality check |
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61 | - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc) |
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62 | - tweaked base frequency filter generation |
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63 | - Normal export (not using readseq) improved: |
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64 | * supports filters and gap removal |
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65 | * optimized for big amount of data |
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66 | * reworked export filters |
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67 | - Display translation with different ORFs in EDIT4 |
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68 | - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse. |
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69 | - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool) |
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70 | - more compact display in EDIT4 |
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71 | - capable to use iso10646 fonts |
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72 | - supports various gcc versions (2.95.3 - 4.1.1) |
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73 | - fixed a bug in DB optimization (occurred when fields had bigger protection than current) |
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74 | - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses |
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75 | different color for size-limited circles; fixed xfig-export-bug |
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76 | - Allows Branchlength <-> Bootstrap value transfer (lossy!) |
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77 | - fixed several scaling bugs in "folded tree"-mode |
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78 | - improved import-filter error-messages |
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79 | - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives |
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80 | several new possibilities: |
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81 | * export taxonomy via 'Export NDS list' |
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82 | * display taxonomy in Editor etc. |
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83 | * display of cascaded taxonomies |
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84 | * display taxonomy of tree_1 in tree_2 |
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85 | * allows to write taxonomy into database field of species |
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86 | * compare taxonomies of two trees |
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87 | * ... |
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88 | - ACI: |
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89 | * many new ACI commands |
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90 | * unified handling of binary ACI-operators |
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91 | * tracing of ACI actions for debugging purpose |
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92 | - ARB Neighbour joining: |
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93 | * bootstrap limit configurable |
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94 | * bugfix: when aborting bootstrap calculation, sometimes no tree was generated |
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95 | - EDIT4: |
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96 | * added unalign right (block-op) |
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97 | * added 'Save loaded properties' |
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98 | - GENE MAP: |
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99 | * multiple views possible at the same time |
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100 | * origin now at "12 o'clock" |
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101 | * implemented 'jump to gene' |
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102 | - tweaked file selection |
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103 | - Enhanced Search Depth for Probe Match --> max 20 MM |
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104 | - CLUSTALW: |
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105 | * separated menus for fast and slow alignment |
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106 | * most parameters accessible from inside ARB now |
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107 | - upgraded to PHYLIP 3.6 (adds PROML) |
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108 | - external programs may be called parallel (e.g. several treeing programs) |
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109 | - fixed bugs in protml and integration of protml |
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110 | - rewrote ASCII database import |
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111 | - arb_repair for databases of any size (script for database repair) |
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112 | - fixed bug in data compression |
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113 | - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse) |
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114 | - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000) |
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115 | - GDE menus cleanup |
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116 | - translation/re-alignment tweaked |
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117 | - unalign right (EDIT4) |
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118 | - visualization of SAIs in Probe Match Results |
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119 | - changed formatting of probe match results; increase # of allowed matches to 100.000; |
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120 | warn if results are truncated |
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121 | - PT server for genes |
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122 | - Probe design performance optimized |
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123 | - fixed NEXUS export format |
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124 | - exports group names into Newick format |
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125 | - import XML tree files |
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126 | - help for external tools now properly shown inside ARB |
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127 | |
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128 | Major changes in Beta 2003_08_22: |
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129 | |
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130 | - automatic formatting of alignments |
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131 | - SECEDIT may use EDIT4 colors |
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132 | - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!)) |
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133 | - updated clustalw to version 1.83 |
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134 | - Restore window sizes for ALL windows (too small sizes are ignored) |
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135 | - new algorithm to add partial sequences to an existing tree |
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136 | - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony |
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137 | - Top area of ARB_NTREE may be reduced to maximize display area |
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138 | - All arb menus may be detached (click dashed line at top of menu) |
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139 | - visualization of SAIs (as background color behind Sequences) |
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140 | - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties |
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141 | - PT-server occupies more memory => does less passes; more diagnostic output |
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142 | - small changes to status window (unhide behavior/time estimation) |
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143 | - menus and menu-hotkeys reorganized |
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144 | - colored buttons in color config windows |
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145 | - alignment concatenation (e.g. several different genes) |
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146 | - merging data of similar species (according selected database field) |
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147 | - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand) |
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148 | - expanded sellists |
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149 | - save/load fixed for multi probes |
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150 | - Binary SAIs are editable in ARB_EDIT4 |
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151 | - Information windows are detachable (allows to have multiple windows showing different items) |
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152 | - Scanning for hidden/unknown database fields improved and separated; |
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153 | possibility to remove unused fields. |
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154 | - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.) |
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155 | - updated fastDNAml to 1.2.2 |
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156 | - added AxML (accelerated fastDNAml 1.2.2) |
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157 | - Field transfer definitions for exporting gene-species |
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158 | - File Selection: - recursive search available |
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159 | - The ARB_NTREE macro recording/execution has been fixed |
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160 | - Colorize species (see demo.arb) |
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161 | - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display |
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162 | - 'IslandHopper' -- a new integrated aligner (beta) |
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163 | - Many improvements and bugfixes to secondary structure editor: |
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164 | * highlighting of search (i.e for probes) like in EDIT4 |
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165 | * interactive constraint editing (stretch/compress) |
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166 | * probe info |
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167 | * editing secondary structure in XFIG now possible |
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168 | * visualization of SAIs |
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169 | - import reads Unix, DOS, and MAC linefeeds |
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170 | - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help |
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171 | - tree and sequence export to XML ( DTDs are provided in ./lib/dtd ) |
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172 | (reloading of these XML files is planned for the future) |
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173 | - fixed problems with phylip-tree import/export (bootstrap values,comments,...) |
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174 | - search in all database fields possible ('[all fields]') |
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175 | - up to 10 quicksaves are kept |
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176 | - new ACI functions: upper, lower, caps, eval |
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177 | - variables for import filter programming |
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178 | - extract gene-species: creates acc; extraction to existing alignments |
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179 | - sequence of selected gene is mirrored in ARB_EDIT4/local_signature |
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180 | (=> selected gene can be highlighted in primary editor) |
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181 | - PCR primer-design for single genes |
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182 | - when selecting a gene, the corresponding gene-species is selected (if found) |
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183 | - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...) |
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184 | - file selection box in import window |
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185 | - mark item with double click works in all search&query windows |
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186 | - User masks: create new; 'edit enable' and 'marked' toggles (like in info window) |
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187 | - Fixed command line help for all Arb-modules |
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188 | - Fixed problem parsing fonts (should fix display problems with default fonts) |
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189 | - Mark mode now works in list-view as well (ARB_NTREE) |
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190 | - Fixed appearance of 'tiny little boxes' (everywhere) |
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191 | - Redesign of ARB help: |
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192 | - a HTML version is in $ARBHOME/lib/help_html |
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193 | - a text version is in $ARBHOME/lib/help (like before, but now generated) |
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194 | |
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195 | Major changes in Beta 2001_11_07: |
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196 | |
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197 | - design probes to maximum length of 60 nucleotides |
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198 | - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode) |
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199 | - import default changed to foreign data format, ali name '16s' |
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200 | - printing of multi-page-trees works again |
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201 | - implemented user defineable masks to access database fields |
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202 | - fixed bugs in pt-server (lockup, unknown species just after building pt-server) |
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203 | - improved performance during pt-server-build |
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204 | - several programs coming along with ARB where updated (PHYLIP,...) |
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205 | - reads EMBL genom files |
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206 | - support for experiments (genom databases only) |
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207 | |
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208 | Major changes in Beta 2001_07_24: |
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209 | |
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210 | - basic support for genoms (Gene Map, reads Genebank files) |
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211 | - ported to libc6 |
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