poy4

ID Status Summary
78 New Select (optimal, unique) not working as expected
77 New -enable-long-sequences is not working
76 Accepted error during wagner builds for annotated data
75 New tree output has two semi-colons at the end of the tree
74 Fixed not_found error when reporting an implied alignment Priority-Medium
73 New not getting consensus reports from a script
72 Fixed Build error in Custom Alphabet files
71 Fixed terminals file: error yes, stopping no Type-Defect
70 Fixed poy 4.1 GUI simple search for jackknife generates bootstraps Type-Defect
69 Fixed Large alphabet error with annotated dataset Type-Defect Priority-Critical
68 Fixed googlecode subversion repository is empty Type-Defect Priority-Medium
67 Fixed diagnosis not reporting changes Type-Defect Priority-Medium
66 Duplicate diagnosis not reporting changes Type-Defect Priority-Medium
65 Fixed Error in iterative documentation Type-Defect Priority-Medium
64 Fixed Add report (searchstats) Type-Enhancement Priority-Medium
63 Fixed inconsistence with example of jackknife in the manual Type-Defect Priority-Medium
62 Fixed Some scripts fail with errors like: Couldn't find 184, 161, 160, 159, 158, 1 My f thread is Error: Not found Type-Defect Priority-Medium Milestone-Release4.0.2874
61 Fixed transform does not modify non-informative non-additive characters Type-Defect Priority-Medium Milestone-Release4.0.2875
60 Fixed report (supports:bremer:"file") outputs an incomplete tree if "file" has a shorter tree than the one for which the support is being printed Type-Defect Priority-Medium Milestone-Release4.0.2871
59 Fixed swap (around) fails Type-Defect Priority-Medium Milestone-Release4.0.2871
58 Fixed poy -e does not quit if POY doesn't find an input file Type-Enhancement Priority-Medium Milestone-Release4.0.2871
57 Fixed transform (static_approx) uses sankoff characters for some tcm's where non-additive characters would be more efficient Type-Enhancement Priority-Medium Milestone-Release4.0.2871
56 Fixed auto_sequence_partition may fail under Type-Defect Priority-Medium Milestone-Release4.0.2871
55 Fixed The order of the fragments may appear inverted in various reports Type-Defect Priority-Medium Milestone-Release4.0.2871
54 Fixed not_found error generated when transform (static_approx) option is used within perturb Type-Defect Priority-Medium
53 Fixed not_found error generated when transform (static_approx) option is used within perturb Type-Defect Priority-Medium
52 Accepted Iterative pass can fail with Tree.Invalid_Node_Id error message Type-Defect Priority-High Milestone-Release4.0
51 Fixed No trees in memory Type-Defect Priority-High Milestone-Release4.0
50 Fixed fuse () may output trees less optimal than the initial trees Type-Defect Priority-Medium Milestone-Release4.0
49 Fixed error during auto_sequence_partition Type-Defect Priority-Critical Milestone-Release4.0
48 Fixed read (prealigned) gives a strange error message when the sequences in the file are not really prealigned. Type-Defect Priority-Medium Milestone-Release4.0
47 Fixed Auto TAB completion of commands in documentation? Type-Enhancement Priority-Medium Milestone-Release4.0 Component-Docs OpSys-All
46 Accepted Using multiple Launchers in the GUI for multiple analyses. Type-Enhancement Priority-Medium Milestone-Release4.1 OpSys-All Component-UI
45 Fixed misspelling in error message Type-Defect Priority-Medium Milestone-Release4.0
44 Fixed "Open POY script" should be "Open POY Launcher" in GUI menu Type-Enhancement Priority-Medium Milestone-Release4.0
43 Fixed Postscript format suggestion in documentation Type-Enhancement Priority-Medium Component-Docs
42 Fixed Underscore in taxon names missing from documentation Type-Enhancement Priority-Medium Component-Docs
41 Fixed tutorials don't correspond Type-Enhancement Priority-Medium Component-Docs Component-Scripts
40 Fixed help (auto_sequence_partition) doesn't retrieve any results Type-Defect Priority-Medium Component-UI Milestone-Release4.0
39 Fixed The documentation for transform commands (for example static_approx), do not clearly explain their behavior inside another command (like swap) Type-Enhancement Priority-Medium Component-Docs
38 Fixed-Partial Bremer support prints maximum integer instead of infinity in some trivial branches Type-Enhancement Priority-Medium Component-UI Milestone-Release4.0.1
37 Fixed select () problem when using branch_and_bound Type-Defect Priority-Medium
36 Fixed Badly formatted trees output Type-Defect Priority-Medium
35 WontFix Number of resampled items in perturb exceeding the number of available items Type-Enhancement Priority-Medium Component-UI
34 Fixed selecting dynamic or static characters does not function Type-Defect Priority-Medium
33 Fixed files with aminoacid data are not included in the cross references report Type-Defect Priority-Medium
32 Fixed not missing is described as not_missing in the documentation Type-Other Priority-Medium Component-Docs
31 Accepted Join Methods and Reroot Order stderr Type-Enhancement Priority-Medium Milestone-Release4.0.1
30 Invalid Perturbing characters Type-Defect Priority-Medium
29 Fixed cost calculation option reports Type-Enhancement Priority-Medium
28 Invalid Incorrect 'ratchet' value order - no stderr error report Type-Defect Priority-Medium
27 Invalid Incorrect 'ratchet' syntax - no stderr error report Type-Defect Priority-Medium
26 Invalid 'perturb' with decimal iterations value - no error reported Type-Defect Priority-Medium
25 Invalid 'perturb' with integer argument cryptic warning Type-Defect Priority-Medium
24 Fixed 'perturb' without loaded trees - insufficient warning Type-Defect Priority-Medium
23 Accepted 'perturb' on one dynamic homology character - no warning issued Type-Enhancement Priority-Low Milestone-Release4.0.1 OpSys-All
22 Fixed Data report when gap opening is used Type-Defect Priority-Medium
21 Accepted IA output Type-Enhancement Priority-Low OpSys-All Milestone-Release4.0.1
20 Fixed Stack overflow error Type-Defect Priority-Medium Milestone-Release4.0
19 WontFix 'Incorrect' data report when 'rename()' command used Type-Other Priority-Medium
18 Fixed the 'all' value of 'cross_references' does not take effect when terminals file is used Type-Defect Priority-Medium
17 Invalid segmentation fault Type-Defect Priority-Medium
16 Fixed Program crashes when "Remove" button is clicked Type-Defect Priority-Medium
15 Fixed jackknife appears to give incorrect value in build 2398 Type-Defect Priority-High
14 Fixed Bootstrap appears to give incorrect support in build2398 Type-Defect Priority-High
13 Accepted Bremer support does not seem to work in build2398 Type-Enhancement Priority-Medium Milestone-Release4.1
12 Duplicate Bremer support does not seem to work in build2398 Type-Enhancement Priority-Medium
11 Fixed problematic symbols used in character/states names (%) Type-Defect Priority-Medium
10 Fixed Error message enhancement request Type-Enhancement Priority-Medium
9 Fixed poy crashes after certain time when executing under lam mpi Type-Other Priority-Medium
8 Fixed Bootstrap support seems too low with static approximation Type-Defect Priority-Medium
7 Fixed Bremer support with static approximation Type-Defect Priority-Medium
6 Fixed Custom alphabet for a DNA sequence yields a higher cost Type-Enhancement Priority-Medium
5 WontFix Bremer support with branch and bound or without swap () Type-Defect Priority-Medium
4 Fixed Nexus file causes error Type-Defect Priority-Medium
3 Fixed Wording change in error message Type-Defect Priority-Medium
2 Fixed Improve the Jackknife and Bootstrap algorithms for tighter support values. Type-Enhancement Priority-Medium Component-Logic Usability
1 Fixed Consensus is not as tight as the input trees imply. Type-Defect Priority-High Milestone-Release4.0