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modified phylodata uploaded 1-08-22
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@j-darocha
j-darocha committed Aug 1, 2022
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2 changes: 1 addition & 1 deletion course_data/phylogeny_typing/1_mafft/input/reference_sars_cov_2.fas
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>EPI_ISL_402124
>EPI_ISL_402124|2019-12-30
attaaaggtttataccttcccaggtaacaaaccaaccaactttcgatctcttgtagatct
gttctctaaacgaactttaaaatctgtgtggctgtcactcggctgcatgcttagtgcact
cacgcagtataattaataactaattactgtcgttgacaggacacgagtaactcgtctatc
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2 changes: 1 addition & 1 deletion course_data/phylogeny_typing/1_mafft/output/sars-cov-2_aln.fas
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>EPI_ISL_402124
>EPI_ISL_402124|2019-12-30
attaaaggtttataccttcccaggtaacaaaccaaccaactttcgatctcttgtagatct
gttctctaaacgaactttaaaatctgtgtggctgtcactcggctgcatgcttagtgcact
cacgcagtataattaataactaattactgtcgttgacaggacacgagtaactcgtctatc
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2 changes: 1 addition & 1 deletion course_data/phylogeny_typing/2_iqtree/input/sars-cov-2_aln.fas
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>EPI_ISL_402124
>EPI_ISL_402124|2019-12-30
attaaaggtttataccttcccaggtaacaaaccaaccaactttcgatctcttgtagatct
gttctctaaacgaactttaaaatctgtgtggctgtcactcggctgcatgcttagtgcact
cacgcagtataattaataactaattactgtcgttgacaggacacgagtaactcgtctatc
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2 changes: 1 addition & 1 deletion course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.contree
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(EPI_ISL_402124:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);
(EPI_ISL_402124_2019-12-30:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);
8 changes: 4 additions & 4 deletions course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.iqtree
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Expand Up @@ -195,7 +195,7 @@ WARNING: 14 near-zero internal branches (<0.0000) should be treated with caution
NOTE: Tree is UNROOTED although outgroup taxon 'EPI_ISL_402124' is drawn at root
Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)

+---EPI_ISL_402124
+---EPI_ISL_402124_2019-12-30
|
| +-----EPI_ISL_12644861_South_Africa_2021-06-14
| +**| (88.6/89)
Expand Down Expand Up @@ -269,7 +269,7 @@ Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)

Tree in newick format:

(EPI_ISL_402124:0.0001657269,((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002339292,(EPI_ISL_6660906_Canada_2021-10-15:0.0010639955,EPI_ISL_6705120_Argentina_2021-10-18:0.0006836458)73.7/92:0.0000238027)88.6/89:0.0000020142,EPI_ISL_7225062_India_2021-05-11:0.0003767165)87.2/92:0.0001060256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100/100:0.0005726789,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000669128,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001340178,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001965879)0/75:0.0000020142,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004366519)0/90:0.0000020142,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003346630)0/94:0.0000020142)100/100:0.0006659807,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002006989)100/100:0.0009279021,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669782,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000669128,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002006857)0/93:0.0000020142)99.8/100:0.0005057804)100/100:0.0009716033)19.1/41:0.0000699059)92.5/78:0.0001348882,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)75.8/68:0.0000317024,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004371733)0/62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001993327)75.7/70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)99.8/100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002702026,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)99.8/100:0.0003000830,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002252296,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)87.6/97:0.0000748573)0/90:0.0000020142)100/100:0.0007028511)89.2/77:0.0000980296,((1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351947,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691537,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005383194,EPI_ISL_8187166_Colombia_2021-02-19:0.0003676294)0/82:0.0000020142,EPI_ISL_8564574_Australia_2021-12-31:0.0004346491)79.7/96:0.0000334556)0/62:0.0000020142)100/100:0.0009754183,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001091051,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0002999642)0/34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)98.1/42:0.0000025527)94.6/98:0.0001808362,EPI_ISL_2493026_Angola_2021-03-22:0.0000664656)100/100:0.0008437994)63.7/32:0.0001312457)0/31:0.0000020299);
(EPI_ISL_402124_2019-12-30:0.0001657269,((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002339292,(EPI_ISL_6660906_Canada_2021-10-15:0.0010639955,EPI_ISL_6705120_Argentina_2021-10-18:0.0006836458)73.7/92:0.0000238027)88.6/89:0.0000020142,EPI_ISL_7225062_India_2021-05-11:0.0003767165)87.2/92:0.0001060256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100/100:0.0005726789,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000669128,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001340178,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001965879)0/75:0.0000020142,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004366519)0/90:0.0000020142,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003346630)0/94:0.0000020142)100/100:0.0006659807,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002006989)100/100:0.0009279021,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669782,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000669128,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002006857)0/93:0.0000020142)99.8/100:0.0005057804)100/100:0.0009716033)19.1/41:0.0000699059)92.5/78:0.0001348882,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)75.8/68:0.0000317024,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004371733)0/62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001993327)75.7/70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)99.8/100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002702026,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)99.8/100:0.0003000830,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002252296,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)87.6/97:0.0000748573)0/90:0.0000020142)100/100:0.0007028511)89.2/77:0.0000980296,((1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351947,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691537,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005383194,EPI_ISL_8187166_Colombia_2021-02-19:0.0003676294)0/82:0.0000020142,EPI_ISL_8564574_Australia_2021-12-31:0.0004346491)79.7/96:0.0000334556)0/62:0.0000020142)100/100:0.0009754183,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001091051,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0002999642)0/34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)98.1/42:0.0000025527)94.6/98:0.0001808362,EPI_ISL_2493026_Angola_2021-03-22:0.0000664656)100/100:0.0008437994)63.7/32:0.0001312457)0/31:0.0000020299);

CONSENSUS TREE
--------------
Expand All @@ -282,7 +282,7 @@ Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)

+--EPI_ISL_402124
+--EPI_ISL_402124_2019-12-30
|
| +----EPI_ISL_12644861_South_Africa_2021-06-14
| +--| (89)
Expand Down Expand Up @@ -357,7 +357,7 @@ Numbers in parentheses are bootstrap supports (%)

Consensus tree in newick format:

(EPI_ISL_402124:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);
(EPI_ISL_402124_2019-12-30:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);

TIME STAMP
----------
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2 changes: 1 addition & 1 deletion course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.log
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ EPI_ISL_7834572|Botswana|2021-12-01 -> EPI_ISL_7834572_Botswana_2021-12-01
1ins:22155g-22163a|EPI_ISL_9419101|India|2022-01-01 -> 1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01

Gap/Ambiguity Composition p-value
1 EPI_ISL_402124 0.00% passed 99.33%
1 EPI_ISL_402124_2019-12-30 0.00% passed 99.33%
2 EPI_ISL_12644861_South_Africa_2021-06-14 0.45% passed 99.99%
3 EPI_ISL_6660906_Canada_2021-10-15 1.19% passed 99.87%
4 EPI_ISL_6705120_Argentina_2021-10-18 0.66% passed 99.98%
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