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Figure 6 | BMC Bioinformatics

Figure 6

From: Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding

Figure 6

Profile Neigbour Joining (PNJ) tree from primary sequence- secondary structure alignment of Nymphaeale ITS2 data using 4SALE and ProfDistS. Simple correction Jukes and Cantor formula (Jukes and Cantor, 1969) operated on sequence-structure alignments. Based on the GTR RNA sequence-structure specific substitution model evolutionary distances between sequence-structure pairs are estimated by maximum likelihood and are also extended on the profile level. The group Hydatellaceae clustered with Cabombaceae and emerged as a sister clade to Nymphaeaceae. Consensus bootstrap values with 100 replicates are shown next to branches and ProfDistS output tree file viewed in NJplot. Tree viewing Profiles are marked by "Pi" (profile generated by identity threshold), "Pb" (profiles generated by bootstrap threshold) and "Po" (old profile generated in a previous iteration).

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BMC Bioinformatics

ISSN: 1471-2105

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