Protml is a main program in molphy for inferring evolutionary trees from protein (amino acid) sequences by using the maximum likelihood method. other programs (c language)
nucml: maximum likelihood inference of nucleic acid phylogeny
protst: basic statistics of protein sequences
nucst: basic statistics of nucleic acid sequences
njdist: neighbor joining phylogeny from distance matrix
utilities (perl)
mollist: get identifiers list molrev: reverse dna sequences
molcat: concatenate sequences molcut: get partial sequences
molmerge: merge sequences nuc2ptn: dna -> amino acid
rminsdel: remove ins/del sites molcodon: get specified codon sites
molinfo: get varied sites mol2mol: molphy format beautifer
inl2mol: interleaved -> molphy mol2inl: molphy -> interleaved
mol2phy: molphy -> sequential phy2mol: sequential -> molphy
must2mol: must -> molphy etc.