Automated phylogeny reconstruction

Methods

• (Prior to inclusion in database: base calling with phred; contig assembly with phrap)
• Progressive multiple sequence alignment with clustalw2
• Maximum likelihood phylogeny estimation from DNA sequences using dnaml (from Joseph Felsenstein’s phylip package; uses a Hidden Markov Model method of inferring rates of evolution)
• DNA similarity using dnadist (F84 algorithm), also from phylip

Primers

• matK-3F_kim
• matK-1R_kim

Settings

• $ clustalw2 -align -output=phylip -outorder=input -type=dna
• $ echo -n "on1nyn" | dnaml
• $ echo -n "yn" | dnadist
• Outgroup added: Amborella trichopoda, GENBANK ID: gi|33333411
• Run time: 2012-05-16 12:10 GMT-0700

dnaml output

Nucleic acid sequence Maximum Likelihood method, version 3.65

phylogeny (newick format)

DNA similarity