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
Settings
- $ clustalw2 -align -output=phylip -outorder=input -type=dna
- $ echo -n "o\n1\ny\n" | dnaml
- $ echo -n "y\n" | 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