category: Sequence - Phylogeny

programs:

• Archaeopteryx - Archaeopteryx is the successor to ATV.
• bltree - bioLegato interface for phylogenetic trees
• confadd - Add confidence information (eg. bootstrap) to a phylogenetic tree
• consense - Consensus trees
• decorator - decorate phylogentic trees with various data fields (such as sequence accessors, taxonomic scientific names) and write them in phyloXML format
• dnacomp - DNA phylogeny using compatability method
• dnadist - Construct distance matrix for DNA sequences
• dnainvar - DNA sequence phylogeny invariants
• dnaml - DNA phylogeny using Maximum Likelihood
• dnamlk - DNA phylogeny using Maximum Likelihood (with evolutionary clock)
• dnamove - DNA parsimony with interactive tree rearrangement
• dnapars - DNA parsimony
• dnapenny - DNA parsimony using branch and bound method
• dollop - Discrete data parsimony method of DOLLO
• drawgram - Draw cladograms
• drawtree - Draw radial trees
• fitch - Distance trees - Fitch/ Margoliash
• kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
• neighbor - Distance trees - Neighbor-Joining/UPGMA
• phylcnv.py - Convert Phylip files to and from other formats
• phyloXMLconverter - convert various phylogentic tree formats to phyloXML
• proml - protein phylogeny using maximum likelihood
• promlk - protein phylogeny by maximum likelihood, constant evolutionary clock
• protdist - Construct distance matrix for protein sequences
• protpars - Protein parsimony
• seqboot - Create resampled datasets
• taxfetch.py - Given a set of ACCESSION numbers create a file containing the corresponding NCBI taxonomy entries
• treedist - Calculate distance between trees