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westram
2025-08-13 10:25
#9
Rev.: 19532
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3271 lines of code changed in 689 files:
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arb_CHANGES.txt (+6 -2)
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GDEHELP/HELP_WRITTEN:
MrBayes.help (+1 -1),
ProbCons.help (+1 -1),
fasttree.help (+1 -1),
muscle.help (+1 -1),
raxml8.help (+2 -2)
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HELP_SOURCE:
Makefile (+14 -8),
arb_help.dtd (+3 -2),
arb_help2xml.cxx (+203 -35),
generate_index.pl (+42 -18),
help.readme (+49),
to_help.xsl (+51 -18),
to_html.xsl (+20 -6)
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HELP_SOURCE/genhelp:
Makefile (+4 -4),
postprocess_genhelp.pl (+41 -8),
standard.header (+4 -4)
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HELP_SOURCE/source:
FAQS.hlp (new),
FORM.hlp (new),
Protection.hlp (+7 -7),
aaali.hlp (new),
accessibility_sai.hlp (new),
aci.hlp (+5 -5),
acisrt.hlp (new),
ad_align.hlp (+7 -7),
ad_extended.hlp (+8 -8),
advice.hlp (+7 -7),
alignment.hlp (new),
ap_stack.hlp (new),
arb.hlp (+18 -18),
arb_commands.hlp (+10 -10),
arb_db.hlp (new),
arb_edit4.hlp (new),
arb_envar.hlp (+7 -7),
arb_export.hlp (new),
arb_export_nds.hlp (+8 -8),
arb_gde.hlp (new),
arb_import.hlp (new),
arb_intro.hlp (+15 -13),
arb_merge.hlp (new),
arb_merge_into.hlp (new),
arb_merge_outof.hlp (+9 -9),
arb_merge_workflow.hlp (new),
arb_ntree.hlp (new),
arb_pars.hlp (new),
arb_pars_init.hlp (+8 -8),
arb_secedit.hlp (new),
asciiprint.hlp (new),
awt_csp.hlp (+7 -7),
bonds.hlp (new),
bootstrap.hlp (new),
branch_analysis.hlp (new),
bugtracker.hlp (new 30),
checkfield.hlp (new),
chimera_check.hlp (new),
cluster_group.hlp (+8 -8),
color.hlp (+11 -11),
color_loadsave.hlp (new),
color_props.hlp (new),
color_props_groups.hlp (new),
color_ranges.hlp (+7 -7),
colorize.hlp (new),
compare_taxonomy.hlp (+7 -7),
compare_topo.hlp (new),
concatenate.hlp (+6 -7),
consense_algo.hlp (+4 -4),
consense_tree.hlp (+8 -8),
consensus.hlp (+10 -10),
consensus_def.hlp (+4 -4),
console.hlp (+5 -5),
copyNpaste.hlp (new),
count_chars.hlp (+7 -7),
csp_2_gnuplot.hlp (+7 -7),
del_list.hlp (new),
di_clusters.hlp (new),
displayField.hlp (new),
dist.hlp (+18 -18),
dssp_ift.hlp (+11 -11),
e4.hlp (new),
e4_background_priority.hlp (new),
e4_block.hlp (new),
e4_consensus.hlp (+7 -7),
e4_defaults.hlp (new),
e4_get_species.hlp (new),
e4_mode.hlp (new),
e4_modsai.hlp (+9 -9),
e4_options.hlp (new),
e4_replace.hlp (+6 -6),
e4_search.hlp (+7 -7),
ecoliref.hlp (new),
ed4_flags.hlp (+6 -6),
ed4_nds.hlp (new),
exec_bug.hlp (new),
experiment_info.hlp (new),
experiment_search.hlp (+7 -7),
export_format.hlp (new),
export_test.hlp (+5 -5),
extended.hlp (+8 -9),
faligner.hlp (new),
field_sel_new.hlp (+8 -8),
field_shader.hlp (new),
gde_flat_ift.hlp (+5 -5),
gde_menus.hlp (new),
gen_create.hlp (+9 -9),
gen_disp_style.hlp (+7 -7),
gen_jump.hlp (+8 -8),
gen_mode.hlp (+5 -5),
gen_new_view.hlp (new),
gen_options.hlp (new),
gene_extract.hlp (new),
gene_hide.hlp (new),
gene_info.hlp (+6 -6),
gene_map.hlp (+8 -8),
gene_mark.hlp (new),
gene_mode.hlp (new),
gene_search.hlp (new),
gene_species.hlp (+10 -10),
gene_species_field_transfer.hlp (new),
gene_species_mark.hlp (new),
genes.hlp (new),
glossary.hlp (+13 -13),
group_by_field.hlp (new),
group_rename.hlp (+7 -7),
group_search.hlp (+5 -5),
group_trees.hlp (+5 -5),
helix.hlp (new),
helixsym.hlp (+10 -10),
help.hlp (new),
import_test.hlp (new),
importift.hlp (+8 -8),
input_mask.hlp (+8 -8),
input_mask_format.hlp (+9 -9),
input_mask_new.hlp (new),
insdel.hlp (+9 -9),
insdel_sai.hlp (new),
islandhopping.hlp (+7 -7),
iupac-codes.hlp (new),
keeled_groups.hlp (+4 -4),
kernlin.hlp (new),
macro.hlp (+7 -7),
man_arb_edit4.hlp (new),
manage_test.hlp (new),
manual.hlp (+5 -5),
mark.hlp (new),
mark_duplicates.hlp (new),
mark_genes.hlp (new),
mark_list.hlp (new),
markbyref.hlp (+5 -5),
matrix_settings.hlp (new),
max_freq.hlp (new),
merge_species.hlp (+7 -7),
mergetaggedfield.hlp (new),
mg_alignment.hlp (new),
mg_extendeds.hlp (new),
mg_names.hlp (+4 -4),
mg_preserve.hlp (+10 -8),
mg_species.hlp (+4 -4),
mg_species_configs.hlp (+8 -8),
mg_trees.hlp (new),
mg_xfer_field_of_listed.hlp (+4 -4),
mg_xfer_field_of_sel.hlp (new),
missbase.hlp (new),
mod_field_list.hlp (+10 -10),
mode.hlp (new),
mode_group.hlp (new),
mode_info.hlp (new),
mode_kernlin.hlp (+9 -9),
mode_length.hlp (+7 -7),
mode_lzoom.hlp (+8 -8),
mode_mark.hlp (+5 -5),
mode_move.hlp (+8 -8),
mode_nni.hlp (+9 -9),
mode_optimize.hlp (+10 -10),
mode_pzoom.hlp (new),
mode_rotate.hlp (new),
mode_select.hlp (new),
mode_setroot.hlp (+8 -8),
mode_spread.hlp (+8 -8),
mode_swap.hlp (+9 -9),
mode_width.hlp (+8 -8),
mode_www.hlp (+8 -8),
move_groups.hlp (new),
mp_params.hlp (+5 -5),
multifurcate.hlp (new),
multiprobe.hlp (+10 -10),
multiproberesults.hlp (+5 -5),
namesadmin.hlp (+6 -6),
ne_align_seq.hlp (+9 -9),
nekey_map.hlp (new),
newwindow.hlp (new),
next_neighbours.hlp (new),
next_neighbours_common.hlp (new),
next_neighbours_listed.hlp (new),
nni.hlp (new),
no_tree.hlp (+6 -10),
nt_align_select.hlp (new),
nt_keys.hlp (+7 -7),
nt_tree_marker_settings.hlp (+5 -5),
nt_tree_select.hlp (new),
nt_tree_settings.hlp (+7 -7),
nt_tree_settings_bootstrap.hlp (+6 -6),
nt_tree_settings_expert.hlp (new),
optimize.hlp (+5 -5),
organism_mark.hlp (new),
organisms.hlp (new),
pa_add.hlp (+7 -7),
pa_bootstrap.hlp (new),
pa_branchlengths.hlp (new),
pa_globopti.hlp (new),
pa_kernlin.hlp (new),
pa_locopti.hlp (new),
pa_mixtree.hlp (new),
pa_optimizer.hlp (new),
pa_partial.hlp (new),
pa_quick.hlp (new),
pa_reset.hlp (new),
pa_value.hlp (+20 -20),
pars.hlp (+9 -10),
partial_sequences.hlp (+7 -7),
pd_match_iupac.hlp (+8 -8),
pd_spec_param.hlp (+8 -8),
pfold.hlp (+9 -9),
pfold_props.hlp (new),
pfold_sai.hlp (+13 -11),
ph_export_markerline.hlp (+7 -7),
phylo.hlp (+9 -9),
pm_spec_param.hlp (+7 -7),
pos_var_pars.hlp (+7 -7),
primer.hlp (new),
primer_new.hlp (+6 -6),
primer_result.hlp (new),
probe_param.hlp (new),
probeadmin.hlp (+8 -8),
probedesign.hlp (+9 -9),
probedesignresult.hlp (+14 -14),
probematch.hlp (+5 -5),
probespec.hlp (+4 -4),
prop_configs.hlp (new),
prop_configs_edit.hlp (new),
props_frame.hlp (+7 -7),
props_nds.hlp (+11 -11),
props_www.hlp (+7 -9),
proteinViewer.hlp (+9 -9),
pt_server.hlp (new),
questions.hlp (+7 -7),
quit.hlp (+7 -7),
realign_dna.hlp (new),
reg.hlp (new),
rename.hlp (+5 -5),
rerepair.hlp (+7 -7),
reset_win_layout.hlp (+7 -7),
resortbyother.hlp (+15 -15),
resorttree.hlp (new),
rna3d_changeMolecule.hlp (new),
rna3d_dispBases.hlp (+9 -9),
rna3d_dispHelices.hlp (+10 -10),
rna3d_dispMolecule.hlp (new),
rna3d_general.hlp (+12 -10),
rna3d_mapSeqData.hlp (new),
rst_log_zoom.hlp (+8 -8),
rst_phys_zoom.hlp (new),
saiProbe.hlp (+7 -7),
saicalc.hlp (+6 -6),
save.hlp (+4 -4),
save_matrix.hlp (new),
savedef.hlp (+7 -7),
scandb.hlp (new),
search_duplicates.hlp (new),
search_equal_fields.hlp (+9 -9),
searching.hlp (new),
sec_bonddef.hlp (+5 -5),
sec_display.hlp (+7 -7),
sec_imexport.hlp (+7 -7),
sec_keys.hlp (+7 -7),
sec_main.hlp (+10 -10),
sec_mode.hlp (+14 -14),
sec_props.hlp (new),
secedit_imexport.hlp (+9 -9),
security.hlp (+8 -8),
sel_box.hlp (new),
sel_fil.hlp (new),
selected.hlp (new),
selected_gene.hlp (new),
seq_quality.hlp (+7 -7),
sequence_colors.hlp (new),
set_color_of_listed.hlp (new),
set_protection.hlp (new),
sina_main.hlp (+6 -7),
sp_IDs.hlp (+5 -5),
sp_del_mrkd.hlp (+9 -9),
sp_info.hlp (new),
sp_info_locked.hlp (+6 -6),
sp_mark.hlp (+8 -8),
sp_search.hlp (new),
sp_sort_fld.hlp (new),
sp_sort_phyl.hlp (+8 -8),
sp_sp_2_ext.hlp (new),
spa_copy.hlp (+4 -4),
spa_create.hlp (new),
spa_delete.hlp (new),
spa_rename.hlp (+4 -4),
spaf_convert.hlp (+7 -7),
spaf_create.hlp (new),
spaf_delete.hlp (+8 -8),
spaf_reorder.hlp (+8 -8),
species.hlp (+4 -4),
species_configs.hlp (+8 -8),
species_configs_highlight.hlp (new),
species_configs_saveload.hlp (+7 -7),
species_join.hlp (+5 -5),
srt.hlp (new),
st_ml.hlp (+6 -6),
submission.hlp (new),
sync_colors.hlp (new),
syncroots.hlp (+5 -5),
syncscroll.hlp (+5 -5),
tags.hlp (+10 -10),
tbl_boot2len.hlp (new),
tbl_justify.hlp (new),
tbl_reset.hlp (new),
tbl_scale.hlp (new),
ted_boot.hlp (+5 -5),
tkeep_mrkd.hlp (+7 -7),
toggle_secinfo.hlp (new),
topology_shader.hlp (+5 -5),
tr_export.hlp (+6 -6),
tr_import.hlp (new),
tr_jump.hlp (+8 -8),
tr_type_dendro.hlp (new 34),
tr_type_irs.hlp (+16 -16),
tr_type_list.hlp (del),
tr_type_nds.hlp (new),
tr_type_radial.hlp (+16 -21),
track_ali_changes.hlp (+7 -7),
trans_anal.hlp (new),
transl_table.hlp (new),
translate_dna_2_pro.hlp (+7 -7),
tree2file.hlp (new),
tree2prt.hlp (+6 -6),
tree_group.hlp (+5 -5),
tree_pseudo.hlp (new),
tree_shading.hlp (new),
treeadm.hlp (+7 -7),
trees.hlp (new),
trm_boot.hlp (new),
trm_del.hlp (new),
trm_mrkd.hlp (new),
undo.hlp (+13 -13),
unittest.hlp (+14 -14),
universal_ift.hlp (new),
unmark_list.hlp (new),
user_matrix.hlp (+8 -8),
version.hlp (+5 -5),
viewdiff.hlp (+8 -8),
visualizeSAI.hlp (+7 -7),
vn_delete.hlp (+4 -4),
vn_import.hlp (new),
vn_search.hlp (new),
vn_suggest.hlp (+8 -8),
write_field_list.hlp (+5 -5),
xferset.hlp (+5 -5),
xterm.hlp (+7 -7)
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HELP_SOURCE/source/prompt:
format_alignments.hlp (new)
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NTREE:
NT_extern.cxx (+5 -10)
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PARSIMONY:
PARS_main.cxx (+1 -1)
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SOURCE_TOOLS:
check_resources.pl (+1)
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UNIT_TESTER/run/help:
unittest.xml (+1 -1)
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XML:
xml.cxx (+2 -1)
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lib/pictures:
help.fig (+14 -15)
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util:
arb_fig (+1 -1)
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westram
2025-08-07 18:50
#8
Rev.: 19517
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1 lines of code changed in 1 file:
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HELP_SOURCE/source:
macro.hlp (+1 -1)
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westram
2025-08-07 18:30
#7
Rev.: 19516
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20 lines of code changed in 2 files:
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HELP_SOURCE/source:
arb_envar.hlp (+3 -3),
macro.hlp (+17 -4)
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westram
2025-08-07 18:27
#6
Rev.: 19515
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16 lines of code changed in 3 files:
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HELP_SOURCE/source:
arb_envar.hlp (+7)
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SH:
arb_launcher (+9 -4)
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westram
2025-08-07 18:24
#5
Rev.: 19514
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34 lines of code changed in 1 file:
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NTREE:
NT_extern.cxx (+34 -32)
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westram
2025-08-02 15:00
#4
Rev.: 19513
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82 lines of code changed in 6 files:
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NTREE:
Makefile (+1),
NT_extern.cxx (+59 -2)
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SL/MACROS:
macro_gui.cxx (+9),
macros.hxx (+1),
trackers.cxx (+10 -2),
trackers.hxx (+2)
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westram
2025-08-01 16:29
#3
Rev.: 19512
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1 lines of code changed in 1 file:
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PERL_SCRIPTS/DB:
databaseReport.pl (+1 -1)
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westram
2025-08-01 16:02
#2
Rev.: 19511
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53 lines of code changed in 1 file:
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PERL_SCRIPTS/DB:
databaseReport.pl (+53 -56)
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westram
2025-08-01 12:09
#1
Rev.: 19510
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1 lines of code changed in 1 file:
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PARSIMONY:
PARS_main.cxx (+1 -1)