trimAl v1.5.0 Summary

# HG changeset patch # User iuc # Date 1732141836 0 # Node ID e379c02027669ff30720a9e64d8b7b2cb8b66f4e # Parent 2a156ec81e7a1829ddaeeb3dd64e02ac88ffc269 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5 diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_example.009.AA.nexus --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_example.009.AA.nexus Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,37 @@ +#NEXUS +BEGIN DATA; + DIMENSIONS NTAX=9 NCHAR=63; +FORMAT DATATYPE=PROTEIN INTERLEAVE=yes GAP=-; +[Name: Csa004271 Len: 63] +[Name: Xtr21234 Len: 63] +[Name: LcaH Len: 63] +[Name: Hsa167996 Len: 63] +[Name: Mmu024661 Len: 63] +[Name: Dre37936 Len: 63] +[Name: LcaM Len: 63] +[Name: Tru14292 Len: 63] +[Name: Ola20972 Len: 63] + +MATRIX +Csa004271 ---------- ----YMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Xtr21234 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +LcaH SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Hsa167996 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Mmu024661 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Dre37936 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +LcaM SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Tru14292 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Ola20972 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL + +Csa004271 EQVKDNLELF DKH +Xtr21234 EQVKDNLELF DKH +LcaH EQVKDNLELF DKH +Hsa167996 EQVKDNLELF DKH +Mmu024661 EQVKDNLELF DKH +Dre37936 EQVKDNLELF DKH +LcaM EQVKDNLELF DKH +Tru14292 EQVKDNLELF DKH +Ola20972 EQVKDNLELF DKH + +; +END; diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_window_example.005.AA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_window_example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_window_example.009.AA.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_window_example.009.AA.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,54 @@ + + + + trimAl v1.5.0 Summary + + + + +

+    Selected Sequences:     6 /Selected Residues:      60
+    Deleted Sequences:      0 /Deleted Residues:       30
+
+    Gaps Scores:           =0=   <.001  <.050  <.100  <.150  <.200  <.250  <.350  <.500  <.750  <1.00   =1=  
+    Similarity Scores:     =0=   <1e-6  <1e-5  <1e-4  <.001  <.010  <.100  <.250  <.500  <.750  <1.00   =1=  
+
+                                 10        20        30        40        50        60        70        80        90
+                         =========+=========+=========+=========+=========+=========+=========+=========+=========+
+    Sp8                  FPWNGLQIHMMGIII---------------------------------------------------------------------------
+    Sp17                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------
+    Sp10                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------------------------------------
+    Sp26                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII------------------------------
+    Sp33                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+    Sp6                  FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+
+    Selected Cols:                                                                                                 
+
+    Gaps Scores:                                                                                                   
+    Similarity Scores:                                                                                             
+

+ + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.out.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.out.phy Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,9 @@ + 6 19 +Sp17 LIGFLLLWQGLDLNKMPVF +Sp10 V--IMLAWLGLEINMMVII +Sp8 Y-GIVLPWNGLQIHMMGII +Sp33 A-GLHMAWGGLEINKQAIL +Sp6 L-GIYLAWLGLEINMMAII +Sp26 L-GLFLAWLGLEINMMAQI + + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.phy Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,8 @@ + 6 60 +Sp17 --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF +Sp10 ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII +Sp8 ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII +Sp33 -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL +Sp6 ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII +Sp26 AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.report.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,54 @@ + + + + trimAl v1.5.0 Summary + + + + +

+    Selected Sequences:     6 /Selected Residues:      19
+    Deleted Sequences:      0 /Deleted Residues:       41
+
+    Gaps Scores:           =0=   <.001  <.050  <.100  <.150  <.200  <.250  <.350  <.500  <.750  <1.00   =1=  
+    Similarity Scores:     =0=   <1e-6  <1e-5  <1e-4  <.001  <.010  <.100  <.250  <.500  <.750  <1.00   =1=  
+
+                                 10        20        30        40        50        60
+                         =========+=========+=========+=========+=========+=========+
+    Sp17                 --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF
+    Sp10                 ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII
+    Sp8                  ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII
+    Sp33                 -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL
+    Sp6                  ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII
+    Sp26                 AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI
+
+    Selected Cols:                                                                   
+
+    Gaps Scores:                                                                     
+    Similarity Scores:                                                               
+

+ + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.stats.txt Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,216 @@ +| Residue % Gaps Gap Score | +| Number | ++----------------------------------------------+ + 0 83.33333333 0.1666666667 + 1 83.33333333 0.1666666667 + 2 83.33333333 0.1666666667 + 3 83.33333333 0.1666666667 + 4 83.33333333 0.1666666667 + 5 83.33333333 0.1666666667 + 6 83.33333333 0.1666666667 + 7 83.33333333 0.1666666667 + 8 83.33333333 0.1666666667 + 9 83.33333333 0.1666666667 + 10 33.33333333 0.6666666667 + 11 16.66666667 0.8333333333 + 12 0 1 + 13 0 1 + 14 0 1 + 15 100 0 + 16 100 0 + 17 100 0 + 18 16.66666667 0.8333333333 + 19 0 1 + 20 0 1 + 21 83.33333333 0.1666666667 + 22 16.66666667 0.8333333333 + 23 0 1 + 24 0 1 + 25 0 1 + 26 0 1 + 27 0 1 + 28 0 1 + 29 0 1 + 30 100 0 + 31 16.66666667 0.8333333333 + 32 66.66666667 0.3333333333 + 33 16.66666667 0.8333333333 + 34 16.66666667 0.8333333333 + 35 66.66666667 0.3333333333 + 36 66.66666667 0.3333333333 + 37 16.66666667 0.8333333333 + 38 16.66666667 0.8333333333 + 39 16.66666667 0.8333333333 + 40 0 1 + 41 83.33333333 0.1666666667 + 42 83.33333333 0.1666666667 + 43 83.33333333 0.1666666667 + 44 83.33333333 0.1666666667 + 45 83.33333333 0.1666666667 + 46 0 1 + 47 0 1 + 48 0 1 + 49 0 1 + 50 0 1 + 51 0 1 + 52 0 1 + 53 0 1 + 54 0 1 + 55 0 1 + 56 0 1 + 57 0 1 + 58 0 1 + 59 0 1 + +| Number of | Cumulative % Cumulative | Number of Gaps % Gaps Gap Score | +| Residues % Length | NumberResid. Length | per Column per Column per Column | ++-------------------------------+---------------------------------------+--------------------------------------------------+ + 27 45 27 45 0 0 1 + 9 15 36 60 1 0.1666666667 0.8333333333 + 1 1.666666667 37 61.66666667 2 0.3333333333 0.6666666667 + 3 5 40 66.66666667 4 0.6666666667 0.3333333333 + 16 26.66666667 56 93.33333333 5 0.8333333333 0.1666666667 + 4 6.666666667 60 100 6 1 0 + +| Residue Similarity | +| Number Value | ++----------------------------+ + 0 0 + 1 0 + 2 0 + 3 0 + 4 0 + 5 0 + 6 0 + 7 0 + 8 0 + 9 0 + 10 5.53110965e-07 + 11 1.646922465e-05 + 12 0.0006768687163 + 13 1.008950312e-05 + 14 0.0002165469632 + 15 0 + 16 0 + 17 0 + 18 2.547356235e-05 + 19 3.554812429e-05 + 20 0.000239324916 + 21 0 + 22 1 + 23 0.004173502792 + 24 1.045452791e-05 + 25 0.17306979 + 26 1.390550642e-05 + 27 1 + 28 4.909260952e-06 + 29 4.015034392e-06 + 30 0 + 31 3.165722228e-05 + 32 4.141910495e-07 + 33 0.01769078523 + 34 0.01232499164 + 35 0.0001380086615 + 36 5.576576978e-10 + 37 1.25446204e-05 + 38 5.194381811e-05 + 39 1 + 40 0.004842269234 + 41 0 + 42 0 + 43 0 + 44 0 + 45 0 + 46 2.948553856e-06 + 47 0.0006762341363 + 48 1 + 49 5.273301213e-06 + 50 1 + 51 1 + 52 0.01518695708 + 53 0.2151376605 + 54 0.02632254921 + 55 0.0008615002735 + 56 0.0174868498 + 57 0.000106244057 + 58 0.001373802545 + 59 0.007171744481 + +| Number of | Cumulative % Cumulative | Similarity | +| Residues % Length | NumberResid. Length | Value | ++-------------------------------+---------------------------------------+----------------+ + 6 10.00000015 6 10.00000015 1 + 1 1.666666754 7 11.66666672 0.2151376605 + 1 1.666666754 8 13.33333403 0.17306979 + 1 1.666666754 9 15.0000006 0.02632254921 + 1 1.666666754 10 16.66666716 0.01769078523 + 1 1.666666754 11 18.33333373 0.0174868498 + 1 1.666666754 12 20.0000003 0.01518695708 + 1 1.666666754 13 21.66666687 0.01232499164 + 1 1.666666754 14 23.33333343 0.007171744481 + 1 1.666666754 15 25 0.004842269234 + 1 1.666666754 16 26.66666806 0.004173502792 + 1 1.666666754 17 28.33333313 0.001373802545 + 1 1.666666754 18 30.00000119 0.0008615002735 + 1 1.666666754 19 31.66666627 0.0006768687163 + 1 1.666666754 20 33.33333433 0.0006762341363 + 1 1.666666754 21 34.9999994 0.000239324916 + 1 1.666666754 22 36.66666746 0.0002165469632 + 1 1.666666754 23 38.33333254 0.0001380086615 + 1 1.666666754 24 40.0000006 0.000106244057 + 1 1.666666754 25 41.66666567 5.194381811e-05 + 1 1.666666754 26 43.33333373 3.554812429e-05 + 1 1.666666754 27 44.99999881 3.165722228e-05 + 1 1.666666754 28 46.66666687 2.547356235e-05 + 1 1.666666754 29 48.33333194 1.646922465e-05 + 1 1.666666754 30 50 1.390550642e-05 + 1 1.666666754 31 51.66666508 1.25446204e-05 + 1 1.666666754 32 53.33333611 1.045452791e-05 + 1 1.666666754 33 55.00000119 1.008950312e-05 + 1 1.666666754 34 56.66666627 5.273301213e-06 + 1 1.666666754 35 58.33333135 4.909260952e-06 + 1 1.666666754 36 60.00000238 4.015034392e-06 + 1 1.666666754 37 61.66666746 2.948553856e-06 + 1 1.666666754 38 63.33333254 5.53110965e-07 + 1 1.666666754 39 64.99999762 4.141910495e-07 + 1 1.666666754 40 66.66666865 5.576576978e-10 + 20 33.33333433 60 100 0 + +## MaxIdentity 0.4474 +#> MaxIdentity Get the maximum identity value for any pair of sequences in the alignment + +## AverageIdentity 0.3056 +#> AverageIdentity Average identity between all sequences + +## Identity sequences matrix +Sp17 1.0000 0.2750 0.2093 0.2750 0.2683 0.2000 +Sp10 0.2750 1.0000 0.4000 0.4054 0.4474 0.3269 +Sp8 0.2093 0.4000 1.0000 0.2500 0.4000 0.2075 +Sp33 0.2750 0.4054 0.2500 1.0000 0.3421 0.2745 +Sp6 0.2683 0.4474 0.4000 0.3421 1.0000 0.3019 +Sp26 0.2000 0.3269 0.2075 0.2745 0.3019 1.0000 + +## AverageMostSimilarIdentity 0.3837 +#> AverageMostSimilarIdentity Average identity between most similar pair-wise sequences + +## Identity for most similar pair-wise sequences matrix +Sp17 0.2750 Sp10 +Sp10 0.4474 Sp6 +Sp8 0.4000 Sp10 +Sp33 0.4054 Sp10 +Sp6 0.4474 Sp10 +Sp26 0.3269 Sp10 + +## MaxOverlap 1.0000 +#> MaxOverlap Get the maximum overlap value for any pair of sequences in the alignment + +## AverageOverlap 0.8723 +#> AverageOverlap Average overlap between all sequences + +## Overlap sequences matrix +Sp17 1.0000 0.8750 0.9250 0.9000 0.9250 0.7250 +Sp10 1.0000 1.0000 1.0000 0.9714 1.0000 0.7714 +Sp8 0.9250 0.8750 1.0000 0.9000 0.9500 0.7750 +Sp33 1.0000 0.9444 1.0000 1.0000 1.0000 0.8056 +Sp6 0.9737 0.9211 1.0000 0.9474 1.0000 0.7632 +Sp26 0.6591 0.6136 0.7045 0.6591 0.6591 1.0000 diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,24 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +------------------------------ + +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +------------------------------ + +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +------------------------------ + +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +------------------------------ + +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +IIIIIIIIIIIIIII--------------- + +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.gappyout.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.gappyout.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.notrim.fasta diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.overlaptrim.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.overlaptrim.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII +>Sp17 +FPWNGLQIHMMGIII +>Sp10 +FPWNGLQIHMMGIII +>Sp26 +FPWNGLQIHMMGIII +>Sp33 +FPWNGLQIHMMGIII +>Sp6 +FPWNGLQIHMMGIII diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.phylip Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,9 @@ + 6 60 +Sp8 FPWNGLQIHMMGIII--------------------------------------------- +Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +Sp10 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +Sp26 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +Sp33 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +Sp6 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.gappyout.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.gappyout.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ + + + + trimAl v1.5.0 Summary + + + + +

+    Selected Sequences:     6 /Selected Residues:      30
+    Deleted Sequences:      0 /Deleted Residues:       60
+
+    Gaps Scores:           =0=   <.001  <.050  <.100  <.150  <.200  <.250  <.350  <.500  <.750  <1.00   =1=  
+
+                                 10        20        30        40        50        60        70        80        90
+                         =========+=========+=========+=========+=========+=========+=========+=========+=========+
+    Sp8                  FPWNGLQIHMMGIII---------------------------------------------------------------------------
+    Sp17                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------
+    Sp10                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------------------------------------
+    Sp26                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII------------------------------
+    Sp33                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+    Sp6                  FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+
+    Selected Cols:                                                                                                 
+
+    Gaps Scores:                                                                                                   
+

+ + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ + + + + trimAl v1.5.0 Summary + + + + +

+    Selected Sequences:     6 /Selected Residues:      60
+    Deleted Sequences:      0 /Deleted Residues:       30
+
+    Gaps Scores:           =0=   <.001  <.050  <.100  <.150  <.200  <.250  <.350  <.500  <.750  <1.00   =1=  
+
+                                 10        20        30        40        50        60        70        80        90
+                         =========+=========+=========+=========+=========+=========+=========+=========+=========+
+    Sp8                  FPWNGLQIHMMGIII---------------------------------------------------------------------------
+    Sp17                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------
+    Sp10                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------------------------------------
+    Sp26                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII------------------------------
+    Sp33                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+    Sp6                  FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+
+    Selected Cols:                                                                                                 
+
+    Gaps Scores:                                                                                                   
+

+ + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.overlaptrim.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.overlaptrim.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ + + + + trimAl v1.5.0 Summary + + + + +

+    Selected Sequences:     6 /Selected Residues:      15
+    Deleted Sequences:      0 /Deleted Residues:       75
+
+    Gaps Scores:           =0=   <.001  <.050  <.100  <.150  <.200  <.250  <.350  <.500  <.750  <1.00   =1=  
+
+                                 10        20        30        40        50        60        70        80        90
+                         =========+=========+=========+=========+=========+=========+=========+=========+=========+
+    Sp8                  FPWNGLQIHMMGIII---------------------------------------------------------------------------
+    Sp17                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------
+    Sp10                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------------------------------------
+    Sp26                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII------------------------------
+    Sp33                 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+    Sp6                  FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+
+    Selected Cols:                                                                                                 
+
+    Gaps Scores:                                                                                                   
+

+ + diff -r 2a156ec81e7a -r e379c0202766 test-data/example.009.AA.out.notrim.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.out.notrim.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,16 @@ +>Csa004271 +----------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEERE +HANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLALHE--T +ANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS---- +>LcaH +---SSQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEERE +HAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDLHKLCS +DHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES-S +>Mmu024661 +MTAPSQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEERE +HAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLELHKLAT +DKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGDES +>Ola20972 +---ESQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKE +HADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDLHKVAS +DHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS-- diff -r 2a156ec81e7a -r e379c0202766 test-data/trimmed_example.009.AA.mega --- a/test-data/trimmed_example.009.AA.mega Mon Nov 18 07:06:34 2024 +0000 +++ b/test-data/trimmed_example.009.AA.mega Wed Nov 20 22:30:36 2024 +0000 @@ -1,5 +1,5 @@ #MEGA -!Title ./test-data/example.009.AA.fasta; +!Title /tmp/saskia/tmpk459g5o_/files/1/8/2/dataset_182865f6-cd70-425d-9a26-7a7fa9974877.dat; !Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard; #Csa004271 diff -r 2a156ec81e7a -r e379c0202766 trimal.xml --- a/trimal.xml Mon Nov 18 07:06:34 2024 +0000 +++ b/trimal.xml Wed Nov 20 22:30:36 2024 +0000 @@ -1,28 +1,82 @@ - + for automated alignment trimming 1.5.0 - 0 + 1 + + topic_3293 + topic_0080 + + + operation_3192 + trimal trimal - - + @@ -31,7 +85,8 @@ - + + @@ -39,13 +94,35 @@ + + + (\d+)([,-]\d+)* + + + (\d+)([,-]\d+)* + + + + + + + + + + + + + + + + @@ -59,9 +136,10 @@ + - + @@ -77,17 +155,22 @@ - + + trimming_mode['mode_selector'] != 'manual' + + + statistics + - + - - + + - + @@ -95,7 +178,55 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - doi:10.1093/bioinformatics/btp348 + 10.1093/bioinformatics/btp348 - \ No newline at end of file +