Accessory application default configurations

Note: If you have an application or a configuration that you would not mind sharing with others, please email me the configuration information out of the AccApp.ini file (apps folder) for that program along with a link to the program (or the program itself) and I will add it to this list.

The following files contain default configuration information for all analysis applications distributed with BioEdit, as well as most PHYLIP programs that take sequence information as input.  Most of the programs below were written by Joe Felsenstein as part of the PHYLIP package.  Configurations for BioEdit utilize unmodified Windows or DOS executables which may also be run independently from the command line.

Most of the PHYLIP programs are not distributed with BioEdit and can be found at Joe Felsenstein's PHYLIP home page

To install any of the programs below, first obtain the program and the associated documentation (if any -- PHYLIP programs each come with an associated .doc file), copy the program and its documentation file into the BioEdit apps folder, download the associated .inf file (below), and run the AccInst program.  Follow the on-screen instructions for the two-step process and the application will be installed with an automated menu link from BioEdit.

Accessory configurations:

Descriptions of PHYLIP programs are taken word-for-word from Joe Felsenstein's PHYLIP home page

To install these configurations, download the AccInst program here.  Note:  These configurations assume that a copy of the program being installed will be in the BioEdit\apps folder.  If they are not, the location of the program will have to be re-specified.
 
Defaults.inf Default configuration for all apps distributed with the BioEdit installation
Cap.inf Cap contig assembly program 
Consense.inf CONSENSE. Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Does NOT compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the PHYLIP package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the PHYLIP package.
Dnacomp.inf DNACOMP. Estimates phylogenies from nucleic acid sequence data using the compatibility criterion, which searches for the largest number of sites which could have all states (nucleotides) uniquely evolved on the same tree. Compatibility is particularly appropriate when sites vary greatly in their rates of evolution, but we do not know in advance which are the less reliable ones.
Dnadist.inf DNADIST. Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, Jin and Nei's distance which allows for rate variation from site to site, and a maximum likelihood method using the model employed in DNAML. The latter method of computing distances can be very slow. (See the PHYLIP Distance Matrix programs pages for information on them).
dnadist_fitch.inf This combination produces a phylogenetic tree from an alignment of DNA sequences by first calculating a distance matrix using DNADIST, then a phylogeny estimate using FITCH
dnadist_neighbor.inf This combination produces a phylogenetic tree from an alignment of DNA sequences by first calculating a distance matrix using DNADIST, then a phylogeny estimate using NEIGHBOR
Dnaml.inf DNAML. Estimates phylogenies from nucleotide sequences by maximum likelihood. The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, with the program inferring which sites have which rates. 
Dnamlk.inf DNAMLK. Same as DNAML but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made. 
Dnamove.inf DNAMOVE. Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the display of reconstructed ancestral bases. This can be used to find parsimony or compatibility estimates by hand.
Dnapars.inf DNAPARS. Estimates phylogenies by the parsimony method using nucleic acid sequences. Allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state.
dnapars_consense.inf Produces a consensus tree by automatically running CONSENSE on the ouput of DNAPARS.
Dnapenny.inf DNAPENNY. Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10 or 11 species. 
fasta3.inf
fasta3.map
Fasta3 from the Fasta package at the University of Virginia -- requires BioEdit version 4.8.4 or newer.  fasta3.map must be present in the BioEdit\apps folder with this default configuration
fastdnaml.inf fastDNAmlis a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program.  fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.  (description taken from the fastDNAml page at CSC).
Fitch.inf FITCH. Estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria. Does not assume an evolutionary clock. This program will be useful with distances computed from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.
Idplot.inf IdPlot is a program to compare sequences in an alignment to a single reference sequence.  All residues in a column that are identical to the reference sequence are changed to a '.'
Kitch.inf KITSCH. Estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria are assumed. This program will be useful with distances computes from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies. 
lalign.inf
lalign.map
Lalign from the Fasta package at the University of Virginia -- requires BioEdit version 4.8.4 or newer.  lalign.map must be present in the BioEdit\apps folder with this default configuration
Neighbor.inf NEIGHBOR. An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets.
Protdist.inf PROTDIST. 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. The distances can then be used in the PHYLIP distance matrix programs.
protdist_fitch.inf This combination produces a phylogenetic tree from an alignment of protein sequences by first calculating a distance matrix using PROTDIST, then a phylogeny estimate using FITCH
protdist_neighbor.inf This combination produces a phylogenetic tree from an alignment of protein sequences by first calculating a distance matrix using PROTDIST, then a phylogeny estimate using NEIGHBOR
Protpars.inf PROTPARS. Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.
protpars_consense.inf Produces a consensus tree by automatically running CONSENSE on the ouput of PROTPARS.
Seqboot.inf SEQBOOT. Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of PHYLIP allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters.