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corneliusroemercorneliusroemer
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Merge pull request #289 from nextstrain/new-clades
Add new clades to phylogenetic
2 parents 64a7476 + 28cbe69 commit 2f88ddb

14 files changed

+301
-8
lines changed

‎nextclade/resources/all-clades/clades.tsv

+55
Original file line numberDiff line numberDiff line change
@@ -73,6 +73,19 @@ C.1.1 clade C.1
7373
C.1.1 nuc 21062 T
7474
C.1.1 nuc 149963 T
7575

76+
E.1 clade C.1.1
77+
E.1 nuc 13563 A
78+
E.1 nuc 121394 T
79+
E.1 nuc 162280 A
80+
81+
E.2 clade C.1.1
82+
E.2 nuc 13563 A
83+
E.2 nuc 151847 A
84+
E.2 nuc 37738 T
85+
86+
E.3 clade C.1.1
87+
E.3 nuc 142797 T
88+
7689
B.1.4 clade B.1
7790
B.1.4 nuc 34308 A
7891

@@ -82,6 +95,12 @@ B.1.5 nuc 70780 T
8295
B.1.6 clade B.1
8396
B.1.6 nuc 111029 A
8497

98+
D.1 clade B.1.6
99+
D.1 nuc 10945 A
100+
D.1 nuc 39515 A
101+
D.1 nuc 44627 T
102+
D.1 nuc 56276 A
103+
85104
B.1.7 clade B.1
86105
B.1.7 nuc 25644 T
87106

@@ -136,10 +155,46 @@ B.1.20 nuc 53326 A
136155
B.1.20 nuc 164385 T
137156
B.1.20 nuc 187620 T
138157

158+
F.1 clade B.1.20
159+
F.1 nuc 11668 A
160+
F.1 nuc 35132 A
161+
F.1 nuc 70414 T
162+
F.1 nuc 70666 T
163+
F.1 nuc 96938 T
164+
165+
F.2 clade B.1.20
166+
F.2 nuc 161629 A
167+
F.2 nuc 22167 T
168+
169+
F.3 clade B.1.20
170+
F.3 nuc 174050 T
171+
F.3 nuc 180618 T
172+
173+
F.4 clade B.1.20
174+
F.4 nuc 34277 T
175+
F.4 nuc 92382 T
176+
F.4 nuc 122551 T
177+
F.4 nuc 126919 A
178+
F.4 nuc 176643 A
179+
180+
F.5 clade B.1.20
181+
F.5 nuc 150831 T
182+
F.5 nuc 126169 A
183+
184+
F.6 clade B.1.20
185+
F.6 nuc 146690 A
186+
F.6 nuc 159608 T
187+
F.6 nuc 168964 A
188+
139189
B.1.21 clade B.1
140190
B.1.21 nuc 22415 A
141191
B.1.21 nuc 132698 T
142192

143193
B.1.22 clade B.1
144194
B.1.22 nuc 34784 T
145195
B.1.22 nuc 101418 T
196+
197+
B.1.23 clade B.1
198+
B.1.23 nuc 27935 A
199+
B.1.23 nuc 64171 G
200+
B.1.23 nuc 73235 T

‎nextclade/resources/all-clades/include_accessions.txt

+1
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@ MK783033 #reference for A.3
77
ON674051 #reference for A.2
88
ON676707 #reference for A.2
99
ON675438 #reference for A.2
10+
OP612690 #reference for A.2
1011
ON676707 #reference for A.2.3
1112
OP555515 #reference for A.2.3
1213
OP450997 #reference for A.2.2

‎nextclade/resources/clade-iib/clades.tsv

+55
Original file line numberDiff line numberDiff line change
@@ -56,6 +56,19 @@ C.1.1 clade C.1
5656
C.1.1 nuc 21062 T
5757
C.1.1 nuc 149963 T
5858

59+
E.1 clade C.1.1
60+
E.1 nuc 13563 A
61+
E.1 nuc 121394 T
62+
E.1 nuc 162280 A
63+
64+
E.2 clade C.1.1
65+
E.2 nuc 13563 A
66+
E.2 nuc 151847 A
67+
E.2 nuc 37738 T
68+
69+
E.3 clade C.1.1
70+
E.3 nuc 142797 T
71+
5972
B.1.4 clade B.1
6073
B.1.4 nuc 34308 A
6174

@@ -65,6 +78,12 @@ B.1.5 nuc 70780 T
6578
B.1.6 clade B.1
6679
B.1.6 nuc 111029 A
6780

81+
D.1 clade B.1.6
82+
D.1 nuc 10945 A
83+
D.1 nuc 39515 A
84+
D.1 nuc 44627 T
85+
D.1 nuc 56276 A
86+
6887
B.1.7 clade B.1
6988
B.1.7 nuc 25644 T
7089

@@ -119,10 +138,46 @@ B.1.20 nuc 53326 A
119138
B.1.20 nuc 164385 T
120139
B.1.20 nuc 187620 T
121140

141+
F.1 clade B.1.20
142+
F.1 nuc 11668 A
143+
F.1 nuc 35132 A
144+
F.1 nuc 70414 T
145+
F.1 nuc 70666 T
146+
F.1 nuc 96938 T
147+
148+
F.2 clade B.1.20
149+
F.2 nuc 161629 A
150+
F.2 nuc 22167 T
151+
152+
F.3 clade B.1.20
153+
F.3 nuc 174050 T
154+
F.3 nuc 180618 T
155+
156+
F.4 clade B.1.20
157+
F.4 nuc 34277 T
158+
F.4 nuc 92382 T
159+
F.4 nuc 122551 T
160+
F.4 nuc 126919 A
161+
F.4 nuc 176643 A
162+
163+
F.5 clade B.1.20
164+
F.5 nuc 150831 T
165+
F.5 nuc 126169 A
166+
167+
F.6 clade B.1.20
168+
F.6 nuc 146690 A
169+
F.6 nuc 159608 T
170+
F.6 nuc 168964 A
171+
122172
B.1.21 clade B.1
123173
B.1.21 nuc 22415 A
124174
B.1.21 nuc 132698 T
125175

126176
B.1.22 clade B.1
127177
B.1.22 nuc 34784 T
128178
B.1.22 nuc 101418 T
179+
180+
B.1.23 clade B.1
181+
B.1.23 nuc 27935 A
182+
B.1.23 nuc 64171 G
183+
B.1.23 nuc 73235 T

‎nextclade/resources/clade-iib/include_accessions.txt

+1
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ MK783033 #reference for A.3
88
ON674051 #reference for A.2
99
ON676707 #reference for A.2
1010
ON675438 #reference for A.2
11+
OP612690 #reference for A.2
1112
ON676707 #reference for A.2.3
1213
OP555515 #reference for A.2.3
1314
OP450997 #reference for A.2.2

‎nextclade/resources/color_ordering.tsv

+11
Original file line numberDiff line numberDiff line change
@@ -239,9 +239,13 @@ lineage B.1.2
239239
lineage B.1.3
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lineage C.1
241241
lineage C.1.1
242+
lineage E.1
243+
lineage E.2
244+
lineage E.3
242245
lineage B.1.4
243246
lineage B.1.5
244247
lineage B.1.6
248+
lineage D.1
245249
lineage B.1.7
246250
lineage B.1.8
247251
lineage B.1.9
@@ -256,8 +260,15 @@ lineage B.1.17
256260
lineage B.1.18
257261
lineage B.1.19
258262
lineage B.1.20
263+
lineage F.1
264+
lineage F.2
265+
lineage F.3
266+
lineage F.4
267+
lineage F.5
268+
lineage F.6
259269
lineage B.1.21
260270
lineage B.1.22
271+
lineage B.1.23
261272
lineage A.2
262273
lineage A.2.1
263274
lineage A.2.2

‎nextclade/resources/include_accessions.txt

+14
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@@ -28,6 +28,20 @@ OQ320441 #reference for B.1.20
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OP539939 #reference for B.1.21
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OQ773522 #reference for B.1.22
3030
OR095023 #reference for B.1.22
31+
PP754993 #reference for B.1.23
32+
PQ036000 #reference for B.1.23
3133
LC753968 #reference for C.1
3234
LC753968 #reference for C.1.1
3335
OR643705 #reference for C.1.1
36+
OR804476 #reference for C.1.1
37+
OQ503831 #reference for D.1
38+
OR804499 #reference for E.1
39+
OR487983 #reference for E.2
40+
OR326991 #reference for E.3
41+
PP533295 #reference for F.1
42+
PQ160003 #reference for F.2
43+
OR473623 #reference for F.3
44+
PP556326 #reference for F.4
45+
PQ160004 #reference for F.5
46+
PP533312 #reference for F.5
47+
OR665162 #reference for F.6

‎nextclade/resources/lineage-b.1/clades.tsv

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@@ -28,6 +28,19 @@ C.1.1 clade C.1
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C.1.1 nuc 21062 T
2929
C.1.1 nuc 149963 T
3030

31+
E.1 clade C.1.1
32+
E.1 nuc 13563 A
33+
E.1 nuc 121394 T
34+
E.1 nuc 162280 A
35+
36+
E.2 clade C.1.1
37+
E.2 nuc 13563 A
38+
E.2 nuc 151847 A
39+
E.2 nuc 37738 T
40+
41+
E.3 clade C.1.1
42+
E.3 nuc 142797 T
43+
3144
B.1.4 clade B.1
3245
B.1.4 nuc 34308 A
3346

@@ -37,6 +50,12 @@ B.1.5 nuc 70780 T
3750
B.1.6 clade B.1
3851
B.1.6 nuc 111029 A
3952

53+
D.1 clade B.1.6
54+
D.1 nuc 10945 A
55+
D.1 nuc 39515 A
56+
D.1 nuc 44627 T
57+
D.1 nuc 56276 A
58+
4059
B.1.7 clade B.1
4160
B.1.7 nuc 25644 T
4261

@@ -91,10 +110,46 @@ B.1.20 nuc 53326 A
91110
B.1.20 nuc 164385 T
92111
B.1.20 nuc 187620 T
93112

113+
F.1 clade B.1.20
114+
F.1 nuc 11668 A
115+
F.1 nuc 35132 A
116+
F.1 nuc 70414 T
117+
F.1 nuc 70666 T
118+
F.1 nuc 96938 T
119+
120+
F.2 clade B.1.20
121+
F.2 nuc 161629 A
122+
F.2 nuc 22167 T
123+
124+
F.3 clade B.1.20
125+
F.3 nuc 174050 T
126+
F.3 nuc 180618 T
127+
128+
F.4 clade B.1.20
129+
F.4 nuc 34277 T
130+
F.4 nuc 92382 T
131+
F.4 nuc 122551 T
132+
F.4 nuc 126919 A
133+
F.4 nuc 176643 A
134+
135+
F.5 clade B.1.20
136+
F.5 nuc 150831 T
137+
F.5 nuc 126169 A
138+
139+
F.6 clade B.1.20
140+
F.6 nuc 146690 A
141+
F.6 nuc 159608 T
142+
F.6 nuc 168964 A
143+
94144
B.1.21 clade B.1
95145
B.1.21 nuc 22415 A
96146
B.1.21 nuc 132698 T
97147

98148
B.1.22 clade B.1
99149
B.1.22 nuc 34784 T
100150
B.1.22 nuc 101418 T
151+
152+
B.1.23 clade B.1
153+
B.1.23 nuc 27935 A
154+
B.1.23 nuc 64171 G
155+
B.1.23 nuc 73235 T

‎phylogenetic/build-configs/ci/config.yaml

+13-2
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@@ -36,9 +36,15 @@ subsample:
3636
- B.1.1
3737
- B.1.2
3838
- B.1.3
39+
- C.1
40+
- C.1.1
41+
- E.1
42+
- E.2
43+
- E.3
3944
- B.1.4
4045
- B.1.5
4146
- B.1.6
47+
- D.1
4248
- B.1.7
4349
- B.1.8
4450
- B.1.9
@@ -53,10 +59,15 @@ subsample:
5359
- B.1.18
5460
- B.1.19
5561
- B.1.20
62+
- F.1
63+
- F.2
64+
- F.3
65+
- F.4
66+
- F.5
67+
- F.6
5668
- B.1.21
5769
- B.1.22
58-
- C.1
59-
- C.1.1
70+
- B.1.23
6071
b1:
6172
group_by: "--group-by country year"
6273
sequences_per_group: "--subsample-max-sequences 100"

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