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• distmat - Create a distance matrix from multiple alignments (part of the EMBOSS package)
• Drawtree - Interactively plot an unrooted tree diagram
• eclique - Obtain the largest cliques of characters and the trees which they suggest using the compatibility method for unrooted two-state characters (part of the EMBOSS package)
• econsense - Create a consensus tree using the majority-rule and strict consensus tree methods (part of the EMBOSS package)
• econtml - Estimate phylogenies by the restricted maximum likelihood using either gene frequencies or continuous characters (part of the EMBOSS package)
• econtrast - Compute contrasts between species for each character (part of the EMBOSS package)
• ednacomp - Find the most parsimonious tree using DNA compatibility (part of the EMBOSS package)
• ednadist - Compute a distance matrix from nucleotide sequences (part of the EMBOSS package)
• ednainvar - Compute phylogenetic invariants from nucleotide sequences (part of the EMBOSS package)
• ednaml - Estimate phylogenies using the maximum likelihood method for DNA sequences (part of the EMBOSS package)
• ednamlk - Estimate phylogenies using the maximum likelihood method for DNA sequences with a molecular clock (part of the EMBOSS package)
• ednapars - Find all of the most parsimonious trees using DNA sequence parsimony criteria (part of the EMBOSS package)
• ednapenny - Find all of the most parsimonious trees using DNA sequence parsimony criteria and the "branch and bound" algorithm (part of the EMBOSS package)
• edollop - Find all of the most parsimonious trees using the Dollo or polymorphism parsimony criteria (part of the EMBOSS package)
• edolpenny - Find all of the most parsimonious trees using the Dollo or polymorphism parsimony criteria and the "branch and bound" algorithm (part of the EMBOSS package)
• efactor - Convert multistate characters to binary characters (part of the EMBOSS package)
• efitch - Calculate distances using the Fitch-Margoliash and Least-Squares methods (part of the EMBOSS package)
• egendist - Compute genetic distances from gene frequencies (part of the EMBOSS package)
• ekitsch - Calculate distances using the Fitch-Margoliash and Least Squares methods with an evolutionary clock (part of the EMBOSS package)
• emix - Find all of the most parsimonious trees using the mixed parsimony methods (part of the EMBOSS package)
• eneighbor - Create a phylogenetic tree using neighbor-joining and UPGMA methods (part of the EMBOSS package)
• epenny - Find all of the most parsimonious trees (part of the EMBOSS package)
• eprotdist - Compute a distance matrix from protein sequences (part of the EMBOSS package)
• eprotpars - Find all of the most parsimonious trees using protein sequence parsimony criteria (part of the EMBOSS package)
• erestml - Create a phylogenetic tree using the maximum likelihood method for restriction sites (part of the EMBOSS package)
• eseqboot - Resample molecular sequence, restriction site, gene frequency or character data using bootstrapping, jackknifing or permutations (part of the EMBOSS package)
• NJplot - Draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package)
• Phyml - Estimate large phylogenies using the maximum likelihood method