PHYLIP DNA parsimony (dnapars) GUI Free Download.
It has been distributed sinceand has over 30, registered users, making it the most pyhlip distributed package of phylogeny programs. It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood.
It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters, and continuous characters. Redistribution and windoows in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code wkndows retain the above copyright notice, this list of conditions and the following windpws.
These include the main documentation file this onewhich you should read fairly completely. In addition there are files for groups of programs, including ones for the molecular sequence programs, the distance phylip free download for windows free programs, the gene frequency and continuous characters programs, the discrete characters programs, and the tree drawing programs.
Finally, each program has its own documentation file. References for the documentation files are all windwos together in по этому сообщению main documentation file.
A good strategy is to: Read this main documentation file. Tentatively decide which programs are of interest to you. Read the documentation files for the groups of programs /32289.txt contain those. Read the documentation files for those individual programs. What The Programs Do Here is a short description of each of the programs. For more detailed discussion you should definitely read the documentation file for the individual program and the documentation file for the group of programs it is in.
In this list the name of each program is a link which will take phylip free download for windows free to the documentation file for that program. Clique Finds the largest clique of mutually compatible characters, phylip free download for windows free the phylogeny which they recommend, for discrete character data with two states. The largest clique перейти на страницу all cliques within a given size range of the largest one are found by a very fast branch and bound search method.
The method does not allow for missing data. For such cases the T Threshold option of Pars or Mix may be a useful alternative.
Compatibility methods are particular useful when some characters are of poor quality and the rest of good quality, but when it is not known in advance which ones are which. Consense Phylip free download for windows free consensus trees by the majority-rule odwnload tree method, which also allows one to easily find the strict consensus tree. Is not able to 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 package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package. Downloqd Estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence phylip free download for windows free due to genetic drift in the absence of new mutations.
Does not assume a molecular clock. An alternative method of analyzing this data is to compute Nei’s genetic distance and use one of the distance matrix programs. This program can also do maximum likelihood analysis of continuous characters that evolve by a Brownian Motion model, but phylip free download for windows free assumes that the characters evolve at equal rates and in an uncorrelated fashion, so that it does not take into account the usual correlations of characters.
Contrast Reads a tree from a tree file, and a data set with continuous characters data, and produces the independent contrasts for those characters, for use in any multivariate statistics package. Will also produce covariances, regressions and correlations between characters for those contrasts. Can also correct for within-species sampling variation when individual phenotypes are available within a population.
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 Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. The distances ffee the Jukes-Cantor formula, downlozd based on Kimura’s 2- parameter method, the F84 model used in Dnaml, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model.
The program can also make a phylip free download for windows free of Dnainvar For nucleic acid sequence data on four species, computes Lake’s and Cavender’s phylogenetic invariants, which test alternative tree downloae. The program also tabulates the phylip free download for windows free of occurrence of the different nucleotide patterns.
Lake’s invariants are the method which he calls « evolutionary parsimony ». Dnaml Estimates phylogenies from nucleotide sequences by maximum likelihood.
The model employed allows for unequal expected forr of the four nucleotides, for unequal rates of transitions and transversions, and for different prespecified rates of change in different categories of sites, and also use windowe a Hidden Markov model of rates, with the жмите inferring which sites have which rates.
This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites. Dnamlk Widnows as Dnaml but assumes a molecular clock. The use of the two phylip free download for windows free together permits a likelihood ratio test of downllad molecular clock dor to be made.
Dowwnload Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the phylpi of reconstructed ancestral bases. This can phylip free download for windows free used ftee find parsimony or compatibility estimates by hand.
Dnapars Estimates frse by the parsimony method using nucleic acid sequences. Allows use the phylip free download for windows free IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state. It can also do transversion parsimony.
Dnapenny Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical depending on the fref for more than species or so. Dollop Estimates phylogenies by нажмите для продолжения Dollo or polymorphism parsimony criteria for discrete character data with two states 0 and 1.
Also reconstructs ancestral states and allows windowws of characters. Dollo parsimony is particularly appropriate for restriction sites data; with ancestor states specified as unknown it may be appropriate for fref fragments data.
Dolmove Interactive construction of phylogenies from discrete character data with two states 0 and 1 приведу ссылку the Dollo or polymorphism parsimony criteria. Evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree.
Dolpenny Finds all most widnows phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of windwos search. May be impractical depending on the data for more than species.
Foe Plots rooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive. It has an interface in the Java language which gives it windws closely similar menu on all three major operating systems. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer such as Postscript or PCL-compatible printerson graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics.
Many of these formats are historic so we no больше на странице have hardware to test them. If you find a problem please report doqnload. Drawtree Similar to Drawgram but plots unrooted phylogenies. It also has a Java interface for previews. Factor Takes discrete multistate data with character state trees and produces the corresponding data set with two states 0 and 1.
Written by Christopher Meacham. This program was formerly used to accomodate multistate characters in Mix, but this is less necessary now that Pars is available. 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 dwnload.
Uses the Fitch-Margoliash criterion and some related least squares criteria, or the Minimum Evolution distance matrix method. Does not assume an evolutionary clock. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.
Gendist Computes one of three different genetic distance formulas from gene frequency data. Fre formulas are Nei’s genetic distance, phyilp Cavalli-Sforza chord measure, and phyli; genetic distance of Reynolds et.
The former is appropriate for data in which new mutations occur in an infinite isoalleles neutral mutation model, the latter two for a model fref mutation and with pure genetic drift. The distances are written to a file in a format appropriate for input to the distance matrix programs. Kitsch Estimates phylogenies pjylip 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, or the Minimum Evolution criterion are possible. This program will be useful with pyhlip computed from molecular sequences, restriction sites or fragments distances, with distances from DNA hybridization measurements, and with genetic distances computed from gene frequencies.
Mix Estimates phylogenies by some parsimony methods for discrete ror data with two states 0 and 1. Allows use of the Нажмите чтобы прочитать больше parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these. Also reconstructs ancestral states and allows weighting of characters does not infer branch lengths.
Move Interactive construction of phylogenies from discrete character data with two states 0 and 1. Neighbor Joining is a distance matrix method producing an unrooted tree without the phylip free download for windows free 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. Pars Multistate discrete-characters parsimony method.
Up to 8 states as well as « ? Cannot do Camin-Sokal or Dollo Parsimony. Can cope with multifurcations, reconstruct ancestral states, use character weights, and infer branch взято отсюда. Penny Finds all most parsimonious phylogenies phylip free download for windows free discrete-character data with two states, for the Wagner, Camin-Sokal, and mixed parsimony criteria using the branch-and-bound method of exact search.
Proml Estimates phylogenies from protein amino acid sequences by maximum likelihood. It also allows different rates of change at known sites.
Download PHYLIP – Phylogeny Inference Package
phylipexe, Self-extracting archive of the Windows executables. Once you download this, click on this file to extract the contents. Download PHYLIP – Infer phylogenies in an effective manner by turning to this comprehensive software solution that packs several tools to.