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Application Name:
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Clique
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Standalone:
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Simple / Advanced Form
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Other:
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This program uses the compatibility method for unrooted two-state characters to obtain the largest cliques of characters and the trees which they suggest.
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A general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
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Application Name:
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Consense
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Standalone:
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Simple / Advanced Form
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Other:
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Construct a consensus tree
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Application Name:
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Dnadist
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Standalone:
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Simple / Advanced Form
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Other:
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Compute distance matrices from nucleotide sequences
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Application Name:
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Dnapars
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Standalone:
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Simple / Advanced Form
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Other:
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This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree. The assumptions of this method are analogous to those of MIX:
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Application Name:
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Dollop
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Standalone:
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Simple / Advanced Form
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Other:
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Carries out the Dollo and polymorphism parsimony methods. The Dollo parsimony method was first suggested in print in verbal form by Le Quesne (1974) and was first well-specified by Farris (1977). The method is named after Louis Dollo since he was one of the first to assert that in evolution it is harder to gain a complex feature than to lose it. The algorithm explains the presence of the state 1 by allowing up to one forward change 0-->1 and as many reversions 1-->0 as are necessary to explain the pattern of states seen. The program attempts to minimize the number of 1-->0 reversions necessary.
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Application Name:
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Drawgram
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Standalone:
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Simple / Advanced Form
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Other:
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Drawgram interactively plots a cladogram- or phenogram-like rooted tree diagram, with many options including orientation of tree and branches, style of tree, label sizes and angles, tree depth, margin sizes, stem lengths, and placement of nodes in the tree. Particularly if you can use your computer to preview the plot, you can very effectively adjust the details of the plotting to get just the kind of plot you want.
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Application Name:
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Drawtree
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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Drawtree interactively plots an unrooted tree diagram, with many options including orientation of tree and branches, label sizes and angles, margin sizes. Particularly if you can use your computer screen to preview the plot, you can very effectively adjust the details of the plotting to get just the kind of plot you want.
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Application Name:
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Fitch
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Standalone:
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Simple / Advanced Form
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Other:
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This program carries out Fitch-Margoliash, Least Squares, and a number of similar methods as described in the documentation file for distance methods.
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Application Name:
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Gibbs
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences
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Application Name:
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Kitsch
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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This program carries out the Fitch-Margoliash and Least Squares methods, plus a variety of others of the same family, with the assumption that all tip species are contemporaneous, and that there is an evolutionary clock (in effect, a molecular clock). This means that branches of the tree cannot be of arbitrary length, but are constrained so that the total length from the root of the tree to any species is the same. The quantity minimized is the same weighted sum of squares described in the Distance Matrix Methods documentation file.
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Application Name:
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Mix
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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Mix is a general parsimony program which carries out the Wagner and Camin-Sokal parsimony methods in mixture, where each character can have its method specified separately. The program defaults to carrying out Wagner parsimony.
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Application Name:
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Neighbor
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Standalone:
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Simple / Advanced Form
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Other:
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This program implements the Neighbor-Joining method of Nei and Saitou (1987) and the UPGMA method of clustering. The program was written by Mary Kuhner and Jon Yamato, using some code from program FITCH. An important part of the code was translated from FORTRAN code from the neighbor-joining program written by Naruya Saitou and by Li Jin, and is used with the kind permission of Dr. Saitou.
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Application Name:
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Pars
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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Pars is a general parsimony program which carries out the Wagner parsimony method with multiple states. Wagner parsimony allows changes among all states. The criterion is to find the tree which requires the minimum number of changes. The Wagner method was originated by Eck and Dayhoff (1966) and by Kluge and Farris (1969). Here are its assumptions:
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Application Name:
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Protdist
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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This program uses protein sequences to compute a distance matrix, under four different models of amino acid replacement. It can also compute a table of similarity between the amino acid sequences. The distance for each pair of species estimates the total branch length between the two species, and can be used in the distance matrix programs Fitch, Kitsch or Neighbor. This is an alternative to using the sequence data itself in the parsimony program Protpars.
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Application Name:
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Protpars
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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This program infers an unrooted phylogeny from protein sequences, using a new method intermediate between the approaches of Eck and Dayhoff (1966) and Fitch (1971). Eck and Dayhoff (1966) allowed any amino acid to change to any other, and counted the number of such changes needed to evolve the protein sequences on each given phylogeny. This has the problem that it allows replacements which are not consistent with the genetic code, counting them equally with replacements that are consistent. Fitch, on the other hand, counted the minimum number of nucleotide substitutions that would be needed to achieve the given protein sequences. This counts silent changes equally with those that change the amino acid.
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Converts input DNA/AA sequence to specified format (Input format is determined automatically).
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Application Name:
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Seqboot
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Standalone:
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Simple / Advanced Form
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Other:
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External Links:
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Seqboot is a general bootstrapping and data set translation tool. It is intended to allow you to generate multiple data sets that are resampled versions of the input data set. Since almost all programs in the package can analyze these multiple data sets, this allows almost anything in this package to be bootstrapped, jackknifed, or permuted. Seqboot can handle molecular sequences, binary characters, restriction sites, or gene frequencies. It can also convert data sets between Sequential and Interleaved format, and into the NEXUS format or into a new XML sequence alignment format.
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