Evolutionary Analysis
EVOLUTIONARY ANALYSIS
TABLE OF CONTENTS
Version 8.1-UNIX
Printed: November 15, 1996 11:44
These programs measure the pairwise homologies between a set of sequences, and provide a conversion to the format required by the Phylip program.
Homologies
Homologies makes a table of the pair-wise distances within a group of aligned sequences.
ToPhylip
ToPhylip writes GCG sequences into a single file in Phylip format.
Phylip2Tree * (+)
Phylip2Tree displays trees computed with one of the PHYLIP-programs in GCG style.
ESeqBoot *
ESeqBoot produces multiple data sets from a molecular sequence data set by bootstrap, jackknife, or permutation resampling.
ESeqBoot is a modified version of the PHYLIP version 3.572c's SEQBOOT, by Joseph Felsenstein, with command line control added.
EDnaML *
EDnaML estimates phylogenies from nucleotide sequences by maximum likelihood.
EDnaML is a modified version of the PHYLIP version 3.572c's DNAML, by Joseph Felsenstein, with command line control added.
EDnaMLK *
EDnaMLK estimates phylogenies from nucleotide sequences by maximum likelihood assuming a molecular clock.
EDnaMLK is a modified version of the PHYLIP version 3.572c's DNAMLK, by Joseph Felsenstein, with command line control added.
EDnaDist *
EDnaDist computes a distance matrix from nucleic acid sequences, under four different models of nucleotide substitution (Jukes and Cantor (1969), Kimura (1980), Jin and Nei(1990) and a model of maximum likelihood (Felsenstein, 1981)).
EDnaDist is a modified version of the PHYLIP version 3.572c's DNADIST, by Joseph Felsenstein, with command line control added.
EProtDist *
EProtDist computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, Kimura's 1983 approximation to it, or a model based on the genetic code plus a constraint on changing to a different category of amino acid.
EProtDist is a modified version of the PHYLIP version 3.572c's PROTDIST, by Joseph Felsenstein, with command line control added.
EDnaPars *
EDnaPars (DNA Sequence Parsimony Method) infers an unrooted phylogeny using nucleic acid sequences.
EDnaPars is a modified version of the PHYLIP version 3.572c's DNAPARS, by Joseph Felsenstein, with command line control added.
EProtPars *
EProtPars (Protein Sequence Parsimony Method) infers an unrooted phylogeny from protein sequences, using a new method intermediate between the approaches of Eck and Dayhoff (1966) and Fitch (1971).
EProtPars is a modified version of the PHYLIP version 3.572c's PROTPARS, by Joseph Felsenstein, with command line control added.
ENeighbor *
ENeighbor estimates phylogenies from distance matrix data using the Neighbor-Joining method or the UPGMA method of clustering.
ENeighbor is a modified version of the PHYLIP version 3.572c's NEIGHBOR, by Joseph Felsenstein, with command line control added.
EFitch *
EFitch estimates phylogenies from distance matrix data using the Fitch-Margoliash method and some related least squares methods.
EFitch is a modified version of the PHYLIP version 3.572c's FITCH, by Joseph Felsenstein, with command line control added.
EKitsch *
EKitsch estimates phylogenies from distance matrix data using the Fitch-Margoliash method and some related least squares methods, with the assumption that there is a evolutionary clock.
EKitsch is a modified version of the PHYLIP version 3.572c's KITSCH, by Joseph Felsenstein, with command line control added.
EConsense *
EConsense computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.
EConsense is a modified version of the PHYLIP version 3.572c's CONSENSE, by Joseph Felsenstein, with command line control added.