Cluster set at subtree whose root is 'Rhodophyta'

Click here to see taxon by cluster Data Availability Matrix
Cluster IDParent clusterTaxIDsGIsLminLmaxMAD1Q2Tcfi3Defline of longest sequenceTree4
0-99116702424369 0.397- 0.000Porphyra suborbiculata specimen voucher WELT A22999 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.-
1-11741651631 0.271- 0.000Porphyra sp. Shinori genes for small subunit ribosomal RNA, ITS1, 5.8S ribosomal RNA, partial and complete sequence, country: Japan:Hokkaido, Hakodate, Shinori.
2-7810781208 0.961- 0.000Porphyra tenera TOP2 gene for type II DNA topoisomerase, partial cds.
3-14303926682398 0.516- 0.000Antithamnion sp. rbcL and rbcS rhodoplast genes for ribulose 1,5 bisphosphate carboxylase large and small subunits.-
5-11119801515 0.767- 0.000A.neglectum chloroplast of cpeA, cpeB, cpeBA genes for phycoerythrin beta subunit.
14-4355521025 0.636- 0.000Porphyra umbilicalis isolate IRE2 18S small subunit ribosomal RNA gene, intron; and His-Cys box protein gene, complete cds.
15-2179524540 0.996- 0.000Mastocarpus stellatus isolate JBLR22 cytochrome oxidase subunit I-like (COI) gene, partial sequence; mitochondrial.
16-49243246 0.998- 0.000Bangia atropurpurea isolate JB238 ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit and ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit genes, partial cds; chloroplast.
19-813495996 0.599- 0.000Porphyra abbottae small subunit ribosomal RNA gene, group IC1 intron, complete sequence.
20-9145671082 0.617- 0.000Porphyra umbilicalis small subunit ribosomal RNA gene, group IC1 intron, complete sequence.
21-2584316949 0.473- 0.000Porphyra sp. strain ROS125 18S ribosomal RNA gene, partial sequence.
22-971481591 0.876- 0.000Porphyra purpurea isolate 543 18S ribosomal RNA gene, partial sequence.
23-66256336 0.872- 0.000Porphyra carolinensis isolate 75 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast gene for chloroplast product.
25-1288033481422 0.540- 0.000Hypnea flexicaulis voucher PH25 cytochrome oxidase subunit I (cox1) gene, partial cds; mitochondrial.
30-22488222250 0.449- 0.000Chondrus crispus Stackouse actin (ChAc) gene, complete cds.
33-10710916732548 0.680- 0.000Bonnemaisonia hamifera elongation factor 2 (EF2) gene, partial cds.
57-412469533 0.950- 0.000Bangia atropurpurea isolate BI12 small subunit ribosomal RNA gene, group IC1 intron, complete sequence.
62-1111317762166 0.715- 0.000Rhodella maculata strain CCMP 736 photosystem I P700 chlorophyll A apoprotein A1 (psaA) gene, partial cds; plastid.
63-2494326191151 0.761- 0.000C.caldarium plastid DNA of psbA gene.
64-151712271266 0.996- 0.000Cyanidium sp. Sybil cave photosystem I P700 chlorophyll a apoprotein A2 (psaB) gene, partial cds; chloroplast.
65-10119331002 0.984- 0.000Cyanidium sp. Sybil cave photosystem II CP43 chlorophyll apoprotein (psbC) gene, partial cds; chloroplast.
66-1112821888 0.987- 0.000Cyanidium sp. Sybil cave photosystem II protein D2 (psbD) gene, partial cds; chloroplast.
67-34567051354 0.701- 0.000Thorea riekei chloroplast tufA gene for elongation factor TU, partial cds.
74-768110512099 0.659- 0.000Antithamnion sp. plastid DNA for 16S rRNA/23S rRNA spacer region and tRNA-Ile and tRNA-Ala genes.
105-99626629 0.999- 0.000Chondrus ocellatus heat shock protein 70 gene, partial cds; chloroplast.
108-4427273219 0.885- 0.000Gracilaria lemaneiformis trehalose-6-phosohate synthase mRNA, complete cds.
171-68103369411 0.956- 0.000Bangia atropurpurea isolate G00033 23S ribosomal RNA gene, partial sequence; plastid.
213-784202245 0.532- 0.000Gracilaria verrucosa polyubiquitin (UBI6R) gene, complete cds.
312-1717407813 0.724- 0.000Cyanidiales sp. CCMEE 5609 macrosatellite sequence; chloroplast.
313-3333468571 0.850- 0.000Galdieria sp. CCMEE 5704 18S ribosomal RNA gene, partial sequence.
314-4646450516 0.930- 0.000Cyanidiales sp. CCMEE 5584 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast.
317-149524103567 0.597- 0.000Reinboldiella schmitziana ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene, partial cds; Rubisco intergenic spacer, complete sequence; and ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene, partial cds; chloroplast genes for chloroplast products.
319-44580674 0.912- 0.000Laurencia cf. perforata 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence.
324-6068714234762 0.360- 0.000Tricleocarpa cylindrica large subunit ribosomal RNA gene, partial sequence.
333-6205151 1.000- 0.000Neosiphonia japonica 19N_japo_Shimoda cpeB-cpeA intergenic spacer, partial sequence; plastid.
334-2646419501 0.975- 0.000Callithamnion corymbosum voucher UTEX LB1950 phycoerythrin beta subunit (cpeB) gene, partial cds; plastid.
335-2645314390 0.969- 0.000Aglaothamnion callophyllidicola voucher C347 phycoerythrin alpha subunit (cpeA) gene, partial cds; plastid.
342-17188171213 0.979- 0.000Aglaothamnion sepositum voucher A152 ATP synthase alpha subunit (atpA) gene, partial cds; plastid.
353-1616303318 0.973- 0.000Ceramium cimbricum 28S large subunit ribosomal RNA gene, partial sequence.
354-46132137 0.977- 0.000Antithamnion kylinii internal transcribed spacer 1, complete sequence.
359-1294100103 0.995- 0.000Ceramium kondoi voucher C157 rbcL/rbcS intergenic spacer, complete sequence; plastid.
364-811623668 0.983- 0.000Ceramium strictum clone CerUK 5.8S ribosomal RNA gene, and internal transcribed spacer 2, partial sequence.
370-53710131013 1.000- 0.000Ceramium californicum voucher AC279 RNA polymerase II largest subunit gene, partial cds.
372-55195267 0.935- 0.000Spyridia clavata isolate PR.E668 ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) genes, partial cds; chloroplast genes for chloroplast products.
390-5813021350 0.992- 0.000Phycodrys setchellii 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 25S ribosomal RNA gene, partial sequence.
392-4155303303 1.000- 0.000Martensia australis voucher YL1558 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
394-517307314 0.997- 0.000Dasysiphonia chejuensis cytochrome oxidase subunit II-like (cox2) gene and cox2-cox3 intergenic spacer, partial sequence; mitochondrial.
399-4149699 0.991- 0.000Galaxaura papillata DNA, internal transcribed spacer 1, partial sequence, clone: G. papillata (Rg).
406-712354901384 0.517- 0.000Gymnogongrus sp. FredericqS_19.i.95_1 isolate 19.i.95 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
429-3142146195 0.780- 0.000Mazzaella japonica isolate JAPONICA internal transcribed spacer 1 and 5.8S ribosomal RNA gene, partial sequence.
431-1447628704 0.963- 0.000Chondracanthus sp. internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence.
432-912147345 0.536- 0.000Dumontia contorta specimen-voucher GWS000762 (UNB) small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
433-489092 0.993- 0.000Iridaea cordata isolate NCU chloroplast rubisco intergenic spacer.
435-47143145 0.993- 0.000Sarcothalia papillosa internal transcribed spacer 1, complete sequence.
451-488971020 0.913- 0.000Sarcodiotheca sp. internal transcribed spacer region , ITS1, 5.8S rRNA gene, and ITS2, complete sequence.
453-46320363 0.973- 0.000Kappaphycus cottonii URP1 region plastid sequence.
458-1019177178 0.997- 0.000Prionitis decipiens ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast.
466-58250243397 0.876- 0.000Gracilaria chilensis isolate BI3 cytochrome oxidase subunit II (cox2) gene, partial cds; and cox2/cox3 intergenic spacer, partial sequence; mitochondrial.
467-550578865 0.806- 0.000Dilsea carnosa strain BM17/85 25S large subunit ribosomal RNA gene, partial sequence.
486-935805968 0.927- 0.000Lemanea fluviatilis isolate WALES7 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
500-77717731 0.987- 0.000G.pristoides 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2, 28S rRNA gene.
502-67196200 0.986- 0.000Gelidium pusillum gene for ITS1, partial sequence.
585-62510831401 0.904- 0.000Gracilaria aff. tepocensis strain Sao Paulo2B 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence.
637-449331140 0.908- 0.000Plocamiocolax pulvinata complete internal transcribed spacer region including ITS 1, 5.8s rDNA and ITS 2.
648-1012617658 0.985- 0.000Polyopes lancifolius ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) genes, partial cds; chloroplast.
650-1339728800 0.961- 0.000Prionitis lanceolata internal transcribed spacer 1, complete sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
656-732363716 0.871- 0.000Pachymenia lusoria collection 1 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence.

  1 Maximum Alignment Density
  2 "Q" alignment comparison score between default Clustal W and Muscle alignments
  3 Level of resolution (consensus fork index) of the strict consensus tree built from the two bootstrap trees from Clustal W and Muscle alignments.
  4 Trees are unrooted majority rule consensus trees from 'fast bootstrap parsimony' algorithm in PAUP* 4.0 using default ClustalW alignments. Expect performance to deteriorate with low MAD or Q scores, large number of taxa, and high sequence divergence (largely owing to alignment problems). Only trees for (taxon) phylogenetically informative clusters with fewer than 1000 sequences are generated.


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