dataset,method,n_clusters,n_cluster_transitions,n_extra_transitions,clusters,transitions
seasonal-flu-h3n2-ha-2016-2018,PCA,8,9,2,"['-1', '0', '1', '2', '3', '4', '5', '6']","[('-1', '5'), ('-1', '6'), ('5', '6'), ('5', '6'), ('-1', '5'), ('5', '4'), ('4', '1'), ('-1', '3'), ('3', '2')]"
seasonal-flu-h3n2-ha-2016-2018,MDS,10,9,0,"['-1', '0', '1', '2', '3', '4', '5', '6', '7', '8']","[('-1', '2'), ('2', '0'), ('2', '3'), ('-1', '8'), ('-1', '1'), ('8', '4'), ('8', '7'), ('8', '6'), ('6', '5')]"
seasonal-flu-h3n2-ha-2016-2018,t-SNE,16,14,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '2', '3', '4', '5', '6', '7', '8', '9']","[('4', '3'), ('4', '8'), ('8', '5'), ('8', '6'), ('8', '9'), ('9', '0'), ('-1', '12'), ('12', '14'), ('14', '13'), ('12', '11'), ('12', '7'), ('12', '10'), ('12', '2'), ('2', '1')]"
seasonal-flu-h3n2-ha-2016-2018,UMAP,7,9,2,"['0', '1', '2', '3', '4', '5', '6']","[('0', '4'), ('4', '3'), ('3', '4'), ('3', '2'), ('3', '5'), ('5', '6'), ('5', '6'), ('6', '1'), ('6', '1')]"
seasonal-flu-h3n2-ha-2016-2018,genetic,9,11,1,"['-1', '0', '1', '2', '3', '4', '5', '6', '7']","[('-1', '0'), ('0', '1'), ('-1', '4'), ('4', '2'), ('4', '7'), ('7', '3'), ('4', '5'), ('5', '4'), ('4', '6'), ('4', '3'), ('4', '7')]"
seasonal-flu-h3n2-ha-2018-2020,PCA,6,4,0,"['-1', '0', '1', '2', '3', '4']","[('2', '0'), ('2', '1'), ('-1', '3'), ('3', '4')]"
seasonal-flu-h3n2-ha-2018-2020,MDS,7,6,1,"['-1', '0', '1', '2', '3', '4', '5']","[('1', '0'), ('1', '2'), ('-1', '5'), ('5', '4'), ('4', '3'), ('4', '3')]"
seasonal-flu-h3n2-ha-2018-2020,t-SNE,8,7,0,"['-1', '0', '1', '2', '3', '4', '5', '6']","[('-1', '5'), ('5', '0'), ('5', '6'), ('6', '2'), ('2', '1'), ('2', '4'), ('4', '3')]"
seasonal-flu-h3n2-ha-2018-2020,UMAP,8,8,0,"['0', '1', '2', '3', '4', '5', '6', '7']","[('4', '0'), ('0', '1'), ('0', '2'), ('4', '5'), ('5', '4'), ('4', '3'), ('3', '7'), ('7', '6')]"
seasonal-flu-h3n2-ha-2018-2020,genetic,5,4,0,"['-1', '0', '1', '2', '3']","[('-1', '0'), ('-1', '2'), ('2', '3'), ('2', '1')]"
seasonal-flu-h3n2-ha-na-2016-2018,PCA (HA only),7,6,0,"['-1', '0', '1', '2', '3', '4', '5']","[('0', '2'), ('2', '1'), ('2', '3'), ('3', '5'), ('5', '3'), ('5', '4')]"
seasonal-flu-h3n2-ha-na-2016-2018,MDS (HA only),9,8,0,"['-1', '0', '1', '2', '3', '4', '5', '6', '7']","[('-1', '0'), ('-1', '2'), ('2', '3'), ('-1', '6'), ('-1', '1'), ('6', '7'), ('6', '4'), ('-1', '5')]"
seasonal-flu-h3n2-ha-na-2016-2018,t-SNE (HA only),16,14,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '2', '3', '4', '5', '6', '7', '8', '9']","[('1', '5'), ('1', '0'), ('5', '7'), ('7', '4'), ('7', '8'), ('7', '6'), ('6', '3'), ('6', '14'), ('14', '13'), ('14', '12'), ('12', '10'), ('12', '11'), ('14', '9'), ('14', '2')]"
seasonal-flu-h3n2-ha-na-2016-2018,UMAP (HA only),7,6,0,"['0', '1', '2', '3', '4', '5', '6']","[('3', '5'), ('3', '2'), ('5', '6'), ('5', '1'), ('5', '4'), ('4', '0')]"
seasonal-flu-h3n2-ha-na-2016-2018,genetic (HA only),9,8,0,"['-1', '0', '1', '2', '3', '4', '5', '6', '7']","[('-1', '1'), ('-1', '0'), ('-1', '2'), ('-1', '3'), ('-1', '4'), ('-1', '5'), ('3', '7'), ('3', '6')]"
seasonal-flu-h3n2-ha-na-2016-2018,PCA (HA/NA),10,9,1,"['-1', '0', '1', '2', '3', '4', '5', '6', '7', '8']","[('0', '8'), ('0', '1'), ('8', '7'), ('8', '6'), ('8', '6'), ('6', '2'), ('2', '3'), ('-1', '5'), ('5', '4')]"
seasonal-flu-h3n2-ha-na-2016-2018,MDS (HA/NA),18,17,2,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '2', '3', '4', '5', '6', '7', '8', '9']","[('-1', '0'), ('-1', '2'), ('2', '1'), ('-1', '8'), ('-1', '6'), ('6', '5'), ('-1', '11'), ('-1', '10'), ('-1', '4'), ('4', '3'), ('-1', '14'), ('14', '15'), ('15', '12'), ('14', '7'), ('7', '9'), ('7', '9'), ('7', '9')]"
seasonal-flu-h3n2-ha-na-2016-2018,t-SNE (HA/NA),18,19,3,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '2', '3', '4', '5', '6', '7', '8', '9']","[('6', '1'), ('6', '5'), ('1', '14'), ('14', '0'), ('14', '13'), ('14', '11'), ('14', '10'), ('14', '2'), ('2', '3'), ('11', '16'), ('16', '15'), ('16', '9'), ('15', '12'), ('11', '4'), ('4', '7'), ('4', '8'), ('4', '8'), ('4', '7'), ('4', '7')]"
seasonal-flu-h3n2-ha-na-2016-2018,UMAP (HA/NA),8,11,3,"['0', '1', '2', '3', '4', '5', '6', '7']","[('0', '3'), ('3', '1'), ('3', '4'), ('4', '2'), ('3', '5'), ('5', '7'), ('7', '6'), ('7', '6'), ('7', '6'), ('7', '6'), ('6', '7')]"
seasonal-flu-h3n2-ha-na-2016-2018,genetic (HA/NA),25,40,10,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '23', '3', '4', '5', '6', '7', '8', '9']","[('-1', '0'), ('-1', '1'), ('1', '2'), ('-1', '3'), ('-1', '13'), ('13', '14'), ('13', '14'), ('-1', '5'), ('5', '6'), ('-1', '3'), ('-1', '11'), ('-1', '15'), ('15', '16'), ('15', '16'), ('15', '16'), ('-1', '19'), ('19', '17'), ('19', '20'), ('19', '7'), ('19', '21'), ('19', '18'), ('19', '12'), ('19', '10'), ('19', '12'), ('19', '21'), ('21', '20'), ('-1', '10'), ('-1', '18'), ('21', '20'), ('20', '18'), ('19', '22'), ('19', '20'), ('20', '19'), ('20', '23'), ('20', '23'), ('-1', '8'), ('8', '9'), ('8', '9'), ('-1', '7'), ('8', '4')]"
sars-cov-2-2020-2022,PCA (Nextstrain clade),4,2,0,"['-1', '0', '1', '2']","[('-1', '0'), ('2', '1')]"
sars-cov-2-2020-2022,MDS (Nextstrain clade),17,23,5,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '2', '3', '4', '5', '6', '7', '8', '9']","[('14', '15'), ('-1', '15'), ('-1', '15'), ('-1', '8'), ('8', '9'), ('9', '8'), ('9', '8'), ('8', '9'), ('9', '8'), ('-1', '6'), ('15', '10'), ('-1', '5'), ('-1', '3'), ('3', '4'), ('-1', '13'), ('-1', '1'), ('-1', '0'), ('-1', '12'), ('-1', '5'), ('-1', '11'), ('13', '12'), ('-1', '2'), ('-1', '7')]"
sars-cov-2-2020-2022,t-SNE (Nextstrain clade),20,18,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '2', '3', '4', '5', '6', '7', '8', '9']","[('8', '18'), ('18', '13'), ('18', '17'), ('-1', '6'), ('18', '7'), ('18', '4'), ('4', '15'), ('4', '3'), ('15', '14'), ('15', '5'), ('15', '9'), ('18', '16'), ('16', '1'), ('1', '0'), ('16', '10'), ('16', '2'), ('16', '12'), ('16', '11')]"
sars-cov-2-2020-2022,UMAP (Nextstrain clade),6,5,0,"['0', '1', '2', '3', '4', '5']","[('3', '4'), ('4', '5'), ('3', '2'), ('2', '1'), ('3', '0')]"
sars-cov-2-2020-2022,genetic (Nextstrain clade),11,11,1,"['-1', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9']","[('5', '9'), ('-1', '7'), ('-1', '4'), ('7', '8'), ('5', '2'), ('-1', '0'), ('5', '3'), ('5', '3'), ('3', '6'), ('5', '1'), ('5', '6')]"
sars-cov-2-2020-2022,PCA (Pango),4,2,0,"['-1', '0', '1', '2']","[('-1', '0'), ('2', '1')]"
sars-cov-2-2020-2022,MDS (Pango),17,23,5,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '2', '3', '4', '5', '6', '7', '8', '9']","[('14', '15'), ('-1', '15'), ('-1', '15'), ('-1', '8'), ('8', '9'), ('9', '8'), ('9', '8'), ('8', '9'), ('9', '8'), ('-1', '6'), ('15', '10'), ('-1', '5'), ('-1', '3'), ('3', '4'), ('-1', '13'), ('-1', '1'), ('-1', '0'), ('-1', '12'), ('-1', '5'), ('-1', '11'), ('13', '12'), ('-1', '2'), ('-1', '7')]"
sars-cov-2-2020-2022,t-SNE (Pango),20,18,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '2', '3', '4', '5', '6', '7', '8', '9']","[('8', '18'), ('18', '13'), ('18', '17'), ('-1', '6'), ('18', '7'), ('18', '4'), ('4', '15'), ('4', '3'), ('15', '14'), ('15', '5'), ('15', '9'), ('18', '16'), ('16', '1'), ('1', '0'), ('16', '10'), ('16', '2'), ('16', '12'), ('16', '11')]"
sars-cov-2-2020-2022,UMAP (Pango),6,5,0,"['0', '1', '2', '3', '4', '5']","[('3', '4'), ('4', '5'), ('3', '2'), ('2', '1'), ('3', '0')]"
sars-cov-2-2020-2022,genetic (Pango),9,9,1,"['-1', '0', '1', '2', '3', '4', '5', '6', '7']","[('-1', '5'), ('5', '4'), ('6', '2'), ('-1', '0'), ('6', '3'), ('6', '3'), ('3', '7'), ('6', '1'), ('6', '7')]"
sars-cov-2-2022-2023,PCA (Nextstrain clade),8,13,5,"['-1', '0', '1', '2', '3', '4', '5', '6']","[('4', '3'), ('4', '3'), ('4', '6'), ('6', '0'), ('6', '0'), ('6', '5'), ('5', '2'), ('6', '4'), ('6', '1'), ('6', '0'), ('6', '0'), ('0', '1'), ('0', '1')]"
sars-cov-2-2022-2023,MDS (Nextstrain clade),19,27,9,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '2', '3', '4', '5', '6', '7', '8', '9']","[('0', '1'), ('1', '0'), ('-1', '9'), ('-1', '4'), ('9', '17'), ('-1', '16'), ('-1', '17'), ('-1', '16'), ('-1', '10'), ('10', '11'), ('10', '11'), ('-1', '14'), ('-1', '14'), ('-1', '13'), ('13', '6'), ('6', '5'), ('-1', '13'), ('-1', '12'), ('-1', '14'), ('-1', '16'), ('-1', '7'), ('-1', '7'), ('-1', '8'), ('-1', '8'), ('-1', '8'), ('-1', '3'), ('3', '2')]"
sars-cov-2-2022-2023,t-SNE (Nextstrain clade),67,68,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '23', '24', '25', '26', '27', '28', '29', '3', '30', '31', '32', '33', '34', '35', '36', '37', '38', '39', '4', '40', '41', '42', '43', '44', '45', '46', '47', '48', '49', '5', '50', '51', '52', '53', '54', '55', '56', '57', '58', '59', '6', '60', '61', '62', '63', '64', '65', '7', '8', '9']","[('-1', '3'), ('-1', '4'), ('-1', '26'), ('26', '18'), ('26', '25'), ('26', '5'), ('5', '0'), ('18', '51'), ('51', '63'), ('63', '44'), ('63', '59'), ('63', '62'), ('63', '38'), ('-1', '57'), ('57', '62'), ('-1', '62'), ('38', '37'), ('37', '32'), ('37', '36'), ('38', '10'), ('10', '61'), ('61', '46'), ('61', '16'), ('61', '17'), ('16', '15'), ('17', '14'), ('14', '13'), ('13', '22'), ('22', '21'), ('61', '56'), ('56', '47'), ('47', '52'), ('52', '23'), ('61', '50'), ('61', '60'), ('61', '55'), ('55', '54'), ('38', '42'), ('42', '43'), ('38', '35'), ('38', '24'), ('38', '9'), ('9', '8'), ('35', '20'), ('35', '34'), ('34', '31'), ('31', '7'), ('7', '6'), ('20', '45'), ('45', '65'), ('65', '64'), ('65', '39'), ('65', '58'), ('-1', '41'), ('65', '29'), ('29', '28'), ('28', '27'), ('28', '19'), ('65', '2'), ('65', '30'), ('30', '33'), ('2', '1'), ('65', '53'), ('65', '49'), ('49', '40'), ('49', '48'), ('49', '11'), ('11', '12')]"
sars-cov-2-2022-2023,UMAP (Nextstrain clade),13,15,0,"['0', '1', '10', '11', '12', '2', '3', '4', '5', '6', '7', '8', '9']","[('3', '8'), ('8', '5'), ('8', '11'), ('11', '12'), ('12', '10'), ('12', '9'), ('9', '7'), ('7', '6'), ('6', '7'), ('7', '4'), ('12', '2'), ('12', '11'), ('12', '6'), ('2', '1'), ('1', '0')]"
sars-cov-2-2022-2023,genetic (Nextstrain clade),17,16,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '2', '3', '4', '5', '6', '7', '8', '9']","[('-1', '2'), ('-1', '1'), ('-1', '13'), ('13', '10'), ('13', '9'), ('9', '11'), ('11', '4'), ('4', '5'), ('5', '6'), ('13', '7'), ('7', '8'), ('13', '12'), ('13', '3'), ('3', '0'), ('12', '14'), ('14', '15')]"
sars-cov-2-2022-2023,PCA (Pango),8,13,5,"['-1', '0', '1', '2', '3', '4', '5', '6']","[('4', '3'), ('4', '3'), ('4', '6'), ('6', '0'), ('6', '0'), ('6', '5'), ('5', '2'), ('6', '4'), ('6', '1'), ('6', '0'), ('6', '0'), ('0', '1'), ('0', '1')]"
sars-cov-2-2022-2023,MDS (Pango),19,27,9,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '2', '3', '4', '5', '6', '7', '8', '9']","[('0', '1'), ('1', '0'), ('-1', '9'), ('-1', '4'), ('9', '17'), ('-1', '16'), ('-1', '17'), ('-1', '16'), ('-1', '10'), ('10', '11'), ('10', '11'), ('-1', '14'), ('-1', '14'), ('-1', '13'), ('13', '6'), ('6', '5'), ('-1', '13'), ('-1', '12'), ('-1', '14'), ('-1', '16'), ('-1', '7'), ('-1', '7'), ('-1', '8'), ('-1', '8'), ('-1', '8'), ('-1', '3'), ('3', '2')]"
sars-cov-2-2022-2023,t-SNE (Pango),67,68,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '23', '24', '25', '26', '27', '28', '29', '3', '30', '31', '32', '33', '34', '35', '36', '37', '38', '39', '4', '40', '41', '42', '43', '44', '45', '46', '47', '48', '49', '5', '50', '51', '52', '53', '54', '55', '56', '57', '58', '59', '6', '60', '61', '62', '63', '64', '65', '7', '8', '9']","[('-1', '3'), ('-1', '4'), ('-1', '26'), ('26', '18'), ('26', '25'), ('26', '5'), ('5', '0'), ('18', '51'), ('51', '63'), ('63', '44'), ('63', '59'), ('63', '62'), ('63', '38'), ('-1', '57'), ('57', '62'), ('-1', '62'), ('38', '37'), ('37', '32'), ('37', '36'), ('38', '10'), ('10', '61'), ('61', '46'), ('61', '16'), ('61', '17'), ('16', '15'), ('17', '14'), ('14', '13'), ('13', '22'), ('22', '21'), ('61', '56'), ('56', '47'), ('47', '52'), ('52', '23'), ('61', '50'), ('61', '60'), ('61', '55'), ('55', '54'), ('38', '42'), ('42', '43'), ('38', '35'), ('38', '24'), ('38', '9'), ('9', '8'), ('35', '20'), ('35', '34'), ('34', '31'), ('31', '7'), ('7', '6'), ('20', '45'), ('45', '65'), ('65', '64'), ('65', '39'), ('65', '58'), ('-1', '41'), ('65', '29'), ('29', '28'), ('28', '27'), ('28', '19'), ('65', '2'), ('65', '30'), ('30', '33'), ('2', '1'), ('65', '53'), ('65', '49'), ('49', '40'), ('49', '48'), ('49', '11'), ('11', '12')]"
sars-cov-2-2022-2023,UMAP (Pango),13,15,0,"['0', '1', '10', '11', '12', '2', '3', '4', '5', '6', '7', '8', '9']","[('3', '8'), ('8', '5'), ('8', '11'), ('11', '12'), ('12', '10'), ('12', '9'), ('9', '7'), ('7', '6'), ('6', '7'), ('7', '4'), ('12', '2'), ('12', '11'), ('12', '6'), ('2', '1'), ('1', '0')]"
sars-cov-2-2022-2023,genetic (Pango),16,15,0,"['-1', '0', '1', '10', '11', '12', '13', '14', '2', '3', '4', '5', '6', '7', '8', '9']","[('-1', '2'), ('-1', '1'), ('-1', '13'), ('13', '10'), ('13', '9'), ('9', '11'), ('11', '4'), ('4', '5'), ('5', '6'), ('13', '7'), ('7', '8'), ('13', '12'), ('13', '0'), ('0', '3'), ('12', '14')]"