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Last change on this file was 11401, checked in by westram, 10 years ago

reintegrates '' into 'trunk':
- consensus trees:
  - support for merging partial trees ("worked" before, but results were crap; implements #65)
  - generated trees are automatically re-rooted and -ordered
  - always list source trees in consensus--comment; show info about partial trees
  - fixed progress bar
- made GBT_TREE a base class of other classes (implements #31)
- save properties in properties (not in )
- new functions 'Remove zombies/marked from ALL trees'
- load/save: layout fixes
- unit tests
  - added tests for basic modifications (PARSIMONY)
- performance:
  - compute_tree updates information in one traversal
  - generators are now capable to generate any type of (w/o needing to copy it once)
- bugfixes:
  - NNI (of marked species) was also always performed for colored species
  - centered beautify-order is stable now
  - improved 'search optimal root'
adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

File size: 1.7 KB

Line
1	ARB_GDE/ARB_GDE.a
2	AWTC/AWTC.a
3	AWTI/AWTI.a
4	CONSENSUS_TREE/CONSENSUS_TREE.a
5	CONVERTALN/CONVERTALN.a
6	DBSERVER/DBSERVER.a
7	DIST/DIST.a
8	EDIT4/EDIT4.a
9	GENOM/GENOM.a
10	GENOM_IMPORT/GENOM_IMPORT.a
11	GL/glAW/libglAW.a
12	HELP_SOURCE/arb_help2xml.o
13	ISLAND_HOPPING/ISLAND_HOPPING.a
14	MERGE/MERGE.a
15	MULTI_PROBE/MULTI_PROBE.a
16	NALIGNER/NALIGNER.a
17	NAMES/NAMES.a
18	NTREE/NTREE.a
19	PARSIMONY/PARSIMONY.a
20	PERLTOOLS/arb_proto_2_xsub.o
21	PHYLO/PHYLO.a
22	PRIMER_DESIGN/PRIMER_DESIGN.a
23	PROBE/PROBE.a
24	PROBE_DESIGN/PROBE_DESIGN.a
25	RNA3D/RNA3D.a
26	SECEDIT/SECEDIT.a
27	SEQ_QUALITY/SEQ_QUALITY.a
28	SERVERCNTRL/SERVERCNTRL.a
29	SL/ALIVIEW/ALIVIEW.a
30	SL/AP_TREE/AP_TREE.a
31	SL/ARB_TREE/ARB_TREE.a
32	SL/AW_HELIX/AW_HELIX.a
33	SL/AW_NAME/AW_NAME.a
34	SL/CB/CB.a
35	SL/DB_QUERY/DB_QUERY.a
36	SL/DB_SCANNER/DB_SCANNER.a
37	SL/DB_UI/DB_UI.a
38	SL/FAST_ALIGNER/FAST_ALIGNER.a
39	SL/FILTER/FILTER.a
40	SL/GUI_ALIVIEW/GUI_ALIVIEW.a
41	SL/HELIX/HELIX.a
42	SL/INSDEL/INSDEL.a
43	SL/ITEMS/ITEMS.a
44	SL/LOCATION/LOCATION.a
45	SL/MACROS/MACROS.a
46	SL/MATRIX/MATRIX.a
47	SL/NDS/NDS.a
48	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a
49	SL/PRONUC/PRONUC.a
50	SL/PTCLEAN/PTCLEAN.a
51	SL/REFENTRIES/REFENTRIES.a
52	SL/REGEXPR/REGEXPR.a
53	SL/ROOTED_TREE/ROOTED_TREE.a
54	SL/SEQIO/SEQIO.a
55	SL/SEQUENCE/SEQUENCE.a
56	SL/TRANSLATE/TRANSLATE.a
57	SL/TREEDISP/TREEDISP.a
58	SL/TREE_ADMIN/TREE_ADMIN.a
59	SL/TREE_READ/TREE_READ.a
60	SL/TREE_WRITE/TREE_WRITE.a
61	STAT/STAT.a
62	TOOLS/arb_consensus_tree.o
63	TOOLS/arb_probe.o
64	TOOLS/arb_test.o
65	WETC/WETC.a
66	XML/XML.a
67	arb_a2ps
68	arb_consensus_tree
69	arb_convert_aln
70	arb_db_server
71	arb_dist
72	arb_dnarates
73	arb_edit4
74	arb_export_rates
75	arb_export_tree
76	arb_gene_probe
77	arb_help2xml
78	arb_message
79	arb_naligner
80	arb_name_server
81	arb_notify
82	arb_ntree
83	arb_pars
84	arb_phylo
85	arb_primer
86	arb_probe
87	arb_pt_server
88	arb_read_tree
89	arb_wetc
90	lib/libARBDB.so
91	lib/libAWT.so
92	lib/libWINDOW.so
93	lib/libCORE.so

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