Phylip Software Free Download – Wakelet
The Philip application was designed to be a small program that fills up your hard drive. Why would I want to do that? There are three reasons. You can usually successfully install programs like this when the hard drive has less than 2 to 4 gigabytes or to megabytes free. With Philip you can test how a program behaves when running on systems with very limited free disk space.
To do this, delete all your personal files and empty your phylip free download for windows free bin. Next, run Philip and tell it to leave 0MB free on your drive. Philip will create a giant file of nonsense information that will wipe out all traces of the old files. Good as new! Why not just copy a bunch of files to my drive instead? It can take phylip free download for windows free long time to copy MB of files to a hard drive- sometimes hours, depending on the source, number, and size of the files.
Philip is optimized for speed and can usually do the trick in just a few minutes. Using the file-copy method makes it tough to achieve an exact amount of free disk space. In Philip, you just enter the number of megabytes you want free and it calculates exactly how large its temporary file needs to be. Fill up your hard drive.
What’s new in Philip 2. Load comments. Philip 2. All rights reserved.
– Index of /phylip/download
It has been distributed since , and has over 30, registered users, making it the most widely distributed package of phylogeny programs. It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices.
It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters, and continuous characters.
University of Washington. All rights reserved. Permission is granted to reproduce, perform, and modify these programs and documentation files. Permission is granted to distribute or provide access to these programs provided that this copyright notice is not removed, the programs are not integrated with or called by any product or service that generates revenue, and that your distribution of these documentation files and programs are free.
Any modified versions of these materials that are distributed or accessible shall indicate that they are based on these programs. Institutions of higher education are granted permission to distribute this material to their students and staff for a fee to recover distribution costs. Permission requests for any other distribution of these programs should be directed to license at u. These include the main documentation file this one , which you should read fairly completely. In addition there are files for groups of programs, including ones for the molecular sequence programs, the distance matrix 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 gathered together in this 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 that 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 you to the documentation file for that program. Clique Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.
The largest clique or 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 Computes consensus trees by the majority-rule consensus 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. Contml Estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is 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 it 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 are the Jukes-Cantor formula, one 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 table of Dnainvar For nucleic acid sequence data on four species, computes Lake’s and Cavender’s phylogenetic invariants, which test alternative tree topologies.
The program also tabulates the frequencies 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 frequencies 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 of a Hidden Markov model of rates, with the program inferring which sites have which rates.
This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites. 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 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 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. 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 data for more than species or so. Dollop Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states 0 and 1. Also reconstructs ancestral states and allows weighting of characters. Dollo parsimony is particularly appropriate for restriction sites data; with ancestor states specified as unknown it may be appropriate for restriction fragments data.
Dolmove Interactive construction of phylogenies from discrete character data with two states 0 and 1 using 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 parsimonious phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of exact search. May be impractical depending on the data for more than species. Drawgram 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 a 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 printers , on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics.
Many of these formats are historic so we no longer have hardware to test them. If you find a problem please report it. 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 species.
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. The formulas are Nei’s genetic distance, the Cavalli-Sforza chord measure, and the 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 without 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 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, or the Minimum Evolution criterion are possible. This program will be useful with distances 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 character data with two states 0 and 1.
Allows use of the Wagner 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 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.
Pars Multistate discrete-characters parsimony method. Up to 8 states as well as “?