Comments (4)
heikotree
commented on August 11, 2024
Very good idea, Rob!
β¦ On 15.02.2022, at 01:42, roblanf ***@***.***> wrote:
Currently we put the really long column (Name) second, which makes it almost unreadable. The fix is easy though - shift the Name column to be the last column.
Here's an example of why this would help. With large (now common) datasets, we currently give users this to look at:
ID Name Type Seq Site Unique Infor Invar Const
1 ES316508nucl_1stpos+ES321882nucl_1stpos+O1187nucl_1stpos+O5959nucl_1stpos+O8818nucl_1stpos+O10353nucl_1stpos+O10353nucl_2ndpos+O10567nucl_1stpos+O10821nucl_1stpos+O11092nucl_1stpos+O11094nucl_1stpos+O11635nucl_1stpos+O11722nucl_1stpos+O13507nucl_1stpos+O13706nucl_1stpos+O14581nucl_1stpos+O15665nucl_1stpos+O16052nucl_1stpos+O16400nucl_1stpos+O17424nucl_1stpos+O19102nucl_1stpos+O21222nucl_1stpos+O21944nucl_1stpos+O22156nucl_1stpos+O22172nucl_1stpos+O22441nucl_1stpos+O23857nucl_1stpos DNA 92 4233 2366 748 2924 2924
2 ES316508nucl_2ndpos+O6843nucl_2ndpos+O7569nucl_2ndpos+O8775nucl_2ndpos+O11722nucl_2ndpos+O13507nucl_2ndpos+O17252nucl_2ndpos+O18599nucl_2ndpos+O19102nucl_2ndpos+O21286nucl_2ndpos+O21944nucl_2ndpos DNA 89 1801 758 130 1556 1556
3 ES316508nucl_3rdpos+ES321806nucl_3rdpos+O540nucl_3rdpos+O988nucl_1stpos+O1187nucl_3rdpos+O8818nucl_3rdpos+O10295nucl_3rdpos+O10600nucl_3rdpos+O10821nucl_3rdpos+O10867nucl_3rdpos+O12201nucl_3rdpos+O13507nucl_3rdpos+O17157nucl_3rdpos+O17252nucl_3rdpos+O17764nucl_3rdpos+O23857nucl_3rdpos DNA 108 2423 2395 2232 120 119
4 ES316890nucl_1stpos+ES319935nucl_1stpos+ES321806nucl_1stpos+ES321879nucl_1stpos+O540nucl_1stpos+O6843nucl_1stpos+O8775nucl_1stpos+O10295nucl_1stpos+O10419nucl_1stpos+O13660nucl_1stpos+O19758nucl_1stpos DNA 110 1495 799 208 1135 1135
5 ES316890nucl_2ndpos+ES319935nucl_2ndpos+ES321879nucl_2ndpos+ES321882nucl_2ndpos+O1187nucl_2ndpos+O5959nucl_2ndpos+O8818nucl_2ndpos+O10419nucl_2ndpos+O10567nucl_2ndpos+O10821nucl_2ndpos+O11092nucl_2ndpos+O11094nucl_2ndpos+O11240nucl_2ndpos+O11569nucl_2ndpos+O11635nucl_2ndpos+O13706nucl_2ndpos+O14581nucl_2ndpos+O16052nucl_2ndpos+O16400nucl_2ndpos+O17424nucl_2ndpos+O19189nucl_2ndpos+O21222nucl_2ndpos+O22156nucl_2ndpos+O22172nucl_2ndpos+O22441nucl_2ndpos+O23857nucl_2ndpos DNA 105 3866 1992 293 2999 2999
6 ES316890nucl_3rdpos+O5959nucl_3rdpos+O11635nucl_3rdpos+O11722nucl_3rdpos+O13706nucl_3rdpos+O14581nucl_3rdpos+O21944nucl_3rdpos+O22156nucl_3rdpos+O22441nucl_3rdpos DNA 83 1353 1347 1262 58 58
7 ES319935nucl_3rdpos+ES321879nucl_3rdpos+ES321882nucl_3rdpos+O6843nucl_3rdpos+O8775nucl_3rdpos+O10419nucl_3rdpos+O11240nucl_3rdpos+O12061nucl_3rdpos+O13660nucl_3rdpos+O18599nucl_3rdpos+O19102nucl_3rdpos+O21286nucl_3rdpos DNA 104 1894 1862 1744 96 96
8 ES321806nucl_2ndpos+O540nucl_2ndpos+O9874nucl_2ndpos+O10295nucl_2ndpos+O10867nucl_2ndpos+O13660nucl_2ndpos+O14147nucl_2ndpos+O15665nucl_2ndpos+O17157nucl_2ndpos+O17764nucl_2ndpos+O19758nucl_2ndpos+O21786nucl_2ndpos+O30441nucl_2ndpos DNA 107 2108 731 40 1955 1955
9 O988nucl_2ndpos+O11240nucl_1stpos+O11569nucl_1stpos+O12061nucl_1stpos+O12201nucl_1stpos+O17252nucl_1stpos+O18599nucl_1stpos+O19058nucl_1stpos+O21286nucl_1stpos DNA 89 1315 871 328 765 765
10 O988nucl_3rdpos+O10353nucl_3rdpos+O12061nucl_2ndpos+O12201nucl_2ndpos+O19058nucl_2ndpos DNA 71 750 450 123 439 439
11 O7569nucl_1stpos+O9874nucl_1stpos+O10867nucl_1stpos+O14147nucl_1stpos+O17157nucl_1stpos+O17764nucl_1stpos+O19189nucl_1stpos+O21786nucl_1stpos+O30441nucl_1stpos DNA 65 1695 763 249 1351 1351
12 O7569nucl_3rdpos+O11094nucl_3rdpos+O14147nucl_3rdpos+O15665nucl_3rdpos+O19058nucl_3rdpos+O19189nucl_3rdpos+O21222nucl_3rdpos DNA 71 1232 1193 1032 103 102
13 O9874nucl_3rdpos+O11092nucl_3rdpos+O11569nucl_3rdpos+O16400nucl_3rdpos+O17424nucl_3rdpos+O21786nucl_3rdpos+O22172nucl_3rdpos+O30441nucl_3rdpos DNA 81 1049 1025 876 96 96
14 O10567nucl_3rdpos+O10600nucl_1stpos+O10600nucl_2ndpos DNA 69 319 243 146 117 117
15 O16052nucl_3rdpos+O19758nucl_3rdpos DNA 48 386 360 301 43 43
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Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max Perutz Labs
Campus Vienna Biocenter 5 (VBC5)
A-1030 Vienna, Austria
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Email: heiko.schmidt(AT)univie.ac.at
Tel. : ++43 +1 / 4277 - 74321
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from iqtree2.
thomaskf
commented on August 11, 2024
Can you please add the header of this section in the iqtree output?
from iqtree2.
roblanf
commented on August 11, 2024
@bqminh the section header is:
SEQUENCE ALIGNMENT
------------------
Input data: 110 taxa with 16 partitions and 25919 total sites (14.9018% missing data)
from iqtree2.
thomaskf
commented on August 11, 2024
Done. This request has been addressed in the branch mf2.
Now the output becomes:
SEQUENCE ALIGNMENT
------------------
Input data: 110 taxa with 19 partitions and 25919 total sites (18.5249% missing data)
ID Type Seq Site Unique Infor Invar Const Name
1 DNA 88 1767 1037 324 1224 1224 ES316508nucl_1stpos+ES321882nucl_1stpos+O5959nucl_1stpos+O6843nucl_1stpos+O8775nucl_1stpos+O13507nucl_1stpos+O16400nucl_1stpos+O19102nucl_1stpos+O21944nucl_1stpos+O22156nucl_1stpos+O23857nucl_1stpos
2 DNA 109 2998 1356 167 2537 2537 ES316508nucl_2ndpos+ES316890nucl_2ndpos+ES319935nucl_2ndpos+ES321806nucl_2ndpos+ES321879nucl_2ndpos+ES321882nucl_2ndpos+O6843nucl_2ndpos+O8775nucl_2ndpos+O10295nucl_2ndpos+O10419nucl_2ndpos+O11092nucl_2ndpos+O11635nucl_2ndpos+O11722nucl_2ndpos+O13507nucl_2ndpos+O13660nucl_2ndpos+O19102nucl_2ndpos+O19189nucl_2ndpos+O21286nucl_2ndpos+O21944nucl_2ndpos+O23857nucl_2ndpos
3 DNA 107 2132 2111 1977 100 100 ES316508nucl_3rdpos+ES321806nucl_3rdpos+O988nucl_1stpos+O1187nucl_3rdpos+O8818nucl_3rdpos+O10600nucl_3rdpos+O10821nucl_3rdpos+O10867nucl_3rdpos+O12061nucl_3rdpos+O12201nucl_3rdpos+O15665nucl_3rdpos+O17252nucl_3rdpos+O17764nucl_3rdpos+O23857nucl_3rdpos
4 DNA 110 2145 1089 325 1626 1626 ES316890nucl_1stpos+ES319935nucl_1stpos+ES321806nucl_1stpos+ES321879nucl_1stpos+O540nucl_1stpos+O10295nucl_1stpos+O10419nucl_1stpos+O13660nucl_1stpos+O14147nucl_1stpos+O17157nucl_1stpos+O17764nucl_1stpos+O19189nucl_1stpos+O19758nucl_1stpos+O21786nucl_1stpos
5 DNA 88 1339 1329 1232 73 73 ES316890nucl_3rdpos+O10295nucl_3rdpos+O11635nucl_3rdpos+O13507nucl_3rdpos+O13706nucl_3rdpos+O14581nucl_3rdpos+O16400nucl_3rdpos+O21944nucl_3rdpos+O22156nucl_3rdpos+O22441nucl_3rdpos
6 DNA 104 1515 1492 1399 70 70 ES319935nucl_3rdpos+ES321879nucl_3rdpos+ES321882nucl_3rdpos+O540nucl_3rdpos+O8775nucl_3rdpos+O10419nucl_3rdpos+O13660nucl_3rdpos+O19102nucl_3rdpos+O21286nucl_3rdpos
7 DNA 84 2021 709 44 1887 1887 O540nucl_2ndpos+O7569nucl_2ndpos+O9874nucl_2ndpos+O10867nucl_2ndpos+O14147nucl_2ndpos+O15665nucl_2ndpos+O17157nucl_2ndpos+O17424nucl_2ndpos+O17764nucl_2ndpos+O19758nucl_2ndpos+O21786nucl_2ndpos+O30441nucl_2ndpos
8 DNA 79 476 346 139 230 230 O988nucl_2ndpos+O11240nucl_1stpos+O19058nucl_1stpos
9 DNA 83 1920 1223 441 1142 1142 O988nucl_3rdpos+O1187nucl_1stpos+O8818nucl_1stpos+O10821nucl_1stpos+O11569nucl_1stpos+O12061nucl_1stpos+O12201nucl_1stpos+O13706nucl_1stpos+O14581nucl_1stpos+O17252nucl_1stpos+O18599nucl_1stpos+O19058nucl_2ndpos+O21286nucl_1stpos
10 DNA 89 2534 1291 219 1932 1932 O1187nucl_2ndpos+O5959nucl_2ndpos+O8818nucl_2ndpos+O10567nucl_2ndpos+O10821nucl_2ndpos+O11094nucl_2ndpos+O11240nucl_2ndpos+O13706nucl_2ndpos+O14581nucl_2ndpos+O16052nucl_2ndpos+O16400nucl_2ndpos+O17252nucl_2ndpos+O21222nucl_2ndpos+O22156nucl_2ndpos+O22172nucl_2ndpos+O22441nucl_2ndpos
11 DNA 67 1153 1127 1006 75 75 O5959nucl_3rdpos+O7569nucl_3rdpos+O11094nucl_3rdpos+O11722nucl_3rdpos+O14147nucl_3rdpos+O17157nucl_3rdpos+O19058nucl_3rdpos
12 DNA 80 428 419 390 27 26 O6843nucl_3rdpos+O11240nucl_3rdpos+O18599nucl_3rdpos
13 DNA 59 674 280 79 574 574 O7569nucl_1stpos+O9874nucl_1stpos+O10867nucl_1stpos+O30441nucl_1stpos
14 DNA 78 948 925 789 88 88 O9874nucl_3rdpos+O11092nucl_3rdpos+O11569nucl_3rdpos+O17424nucl_3rdpos+O21786nucl_3rdpos+O22172nucl_3rdpos+O30441nucl_3rdpos
15 DNA 75 1070 473 135 785 785 O10353nucl_1stpos+O10353nucl_2ndpos+O10567nucl_1stpos+O11092nucl_1stpos+O16052nucl_1stpos+O21222nucl_1stpos
16 DNA 88 901 545 142 608 608 O10353nucl_3rdpos+O11569nucl_2ndpos+O12061nucl_2ndpos+O12201nucl_2ndpos+O18599nucl_2ndpos+O22172nucl_1stpos+O22441nucl_1stpos
17 DNA 69 319 243 146 117 117 O10567nucl_3rdpos+O10600nucl_1stpos+O10600nucl_2ndpos
18 DNA 72 757 388 104 579 579 O11094nucl_1stpos+O11635nucl_1stpos+O11722nucl_1stpos+O15665nucl_1stpos+O17424nucl_1stpos
19 DNA 58 822 780 654 83 83 O16052nucl_3rdpos+O19189nucl_3rdpos+O19758nucl_3rdpos+O21222nucl_3rdpos
from iqtree2.
Related Issues (20)
- can iqtree2 handle 6 million genomes of SARS-CoV-2? HOT 2
- 11 weight for 12.12 model & rate parameters for each site HOT 6
- IQ-TREE not working on M1 macbook HOT 2
- Unexplained base content of sequence alignment generated under UNREST model HOT 1
- IQTree crashes with nonreversible models HOT 2
- crashing during model selection HOT 2
- Ambiguous bases being treated as constant HOT 1
- Help with IQ-TREE HOT 3
- Constraint not compatible with ModelFinder? HOT 5
- Segmentation fault when trying to use lds2 with predefined substitution rates HOT 2
- CMake deprecation warning: Compatibility with CMake < 3.5 will be removed from a future version of CMake.
- Build fails on ARM Mac (macOS 14) with `Error at CMakeLists.txt:701 (add_subdirectory)` HOT 4
- IQtree help string should mention architecture HOT 1
- Cannot find exact build setup used to make the release binaries HOT 1
- auto thread number detection with modelfinder HOT 1
- Compilation failure with GCC 12 HOT 8
- A question that how to gene tree root on my dataοΌ HOT 3
- Compliation error HOT 6
- A possible bug? HOT 8
- Enhancement request: Implement +ASC option to speed up MixtureFinder searches on supermatrices lacking constant sites HOT 3
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