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Incomplete (contain fewer than 79 of 79 core marker genes, a gene being considered

as present only if the query cover is greater than 40%):

Marker genes
Candidatus Atelocyanobacterium thalassa ALOHA=UCYN-A1 CP001842
Cyanobiont of Braarudosphaera bigelowii CPSB-1 AP024987
Desikacharya piscinale CENA21 CP012036
Gloeomargarita lithophora D10 CP017675
Leptolyngbya 7M CP070897 (sp.) 72
Leptolyngbya 15MV CP071923 (sp.) 66

Chimeric (segments from two different cyanobacteria),

or poor sequences seriously disturbing tree topology:

Richelia sinica FACHB-800 CP021056

Duplicate (re-assembled or re-sequenced) genomes:

Anabaena PCC 7122 AP018166 (sp.)
Synechococcus WH 8101 CP047932 (sp.)
Synechocystis PCC 6803 CP003265 (sp.)
Synechocystis PCC 6803 BA000022 (sp.)

To prune the tree, removed genomes from clades that are over-represented:

Strains of the OMF taxa:

A15-127 (CP047948), A18-25c (CP047957), A15-24 (CP047960), A15-44 (CP047938),
A15-60 (CP047933), A15-62 (CP047950), A18-40 (CP047956), BIOS-U3-1 (CP047936)
BMK-MC-1 (CP047939), M16-1 (CP047954), M30B3 (CP073761), MEDNS5 (CP047952),
Minos11 (CP047953), MVIR-18-1 (CP047942), NS01 (CP047940),
NOUM97013 (CP047941), PROS-7-1 (CP047945), PROS-9-1 (CP047961),
PROS-U-1 (CP047951), ROS8604 (CP047946), RS9902 (CP047949), RS9907 (CP047944),
RS9909 (CP047943), SYN20 (CP047959), TAK9802 (CP047937)