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PHYLIP, which stands for "The PHYLogeny Inference Package, is a collection of applications that were developed to help advanced computer users such as genetics engineers or scientists in related fields infer evolutionary trees (phylogenies).
Among the methods that can be found in the package you can find parsimony, likelihood methods such as bootstrapping and consensus trees, as well as distance matrix.
The types of data that can be handled by these applications include gene frequencies, distance matrices, molecular sentences, restriction sites and fragments and discrete characters.
The tools can be easily controlled via a menu, which prompts the user to configure the options beforehand and then enables them to start computing the data. Information is accessed by the program from a text document on the computer, which can be prepared in advance by using any text editor or word processor.
It is worth mentioning that in order to use text documents from the PC, users must save them as flast ASCII or Text Only formats, as proprietary formats don't work at all when you try to import them.
Some programs are able to write data files in the PHYLIP format. Most of the tools attempt to identify data in a document called "infile." In case this document is not found, they prompt the user to type the name of the data file manually.

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PHYLIP is intended to run on PCs with a standard amount of memory and a standard text editor.
The package consists of three levels of analysis, which are described in a bottom-up approach, as opposed to a top-down.
The package is arranged such that the first level contains two applications, Distmat and Consense, which are called by the second level, Dendro. This second level contains five applications, which are DnaA, Fitch, Ngen, Patl and Neighbor.
The individual commands of the Dendro package are accessed by an external menu, which is called Dendro Menu.
Within this level you can find the most basic menu command, called GeneOrder, which enables you to compute the pairwise distances among sequences.
The Dendro Package Contains the Following Tools and Applications:
1. – Distmat: A distance matrix computation algorithm.
2. – Consense: An application that is used to compute consensus trees by reducing the number of parsimony steps.
3. – Dnaa: This is an application for computing the pairwise distance among DNA sequences.
4. – Fitch: This is an application for computing phylogenetic trees by modifying the method of J. Fitch, which makes it more suitable for small data sets, which vary in size from only 2 to 10 numbers.
5. – Ngen: This is an application for inferring phylogenetic trees via neighbor joining.
6. – Patl: This is an application for counting the number of parsimony steps required to reach a particular tree.
7. – Neighbor: This is an application for computing neighbor trees.
After the preliminary data and application setup stage, the package allows you to save the alignment in the PHYLIP format, which is the main form that is accepted as input for the software.
The PHYLIP package was written by Keith Goyette, based on the work of Jonathan Fitch. It has been included in UNIX and DOS versions. Some of its main objectives include being easy to use, easy to understand and easy to modify.
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PHYLIP is a collection of programs for reconstructing evolutionary trees for a given set of homologous sequences.
It is a robust and reliable software package that can be used by everyone with an interest in phylogeny.
PHYLIP was designed to allow users to reconstruct a single tree or to compare and optimise many trees using different methods.
PHYLIP is a program, which begins its operations by extracting molecular data from an ASCII file, which contains the information about the homologous sequences.

PHYLIP v2.5 is available as an independent package that is compatible with any modern Macintosh.
The PHYLIP family of programs are based on the PHYLIP system, which is a new method for both reconstructing evolutionary trees and comparing and optimising them, without getting stuck in local optima.

SuperTree v2.0 runs on any version of Windows, and relies on the PHYLIP 2.5 library.
SuperTree is an application that allows users to compare up to 12 trees and to reconstruct the most likely one.
Reconstructing an evolutionary tree from the sequences in a set of homologous genes is a common and useful method of inferring phylogeny.
It is a powerful and robust software, which provides a basis for evolutionary studies, and allows individuals who cannot have access to computers but can use Internet to find out their place in the biological world.
Applications like PHYLIP allow biologists to easily run the analysis of a large number of homologous sequences by inferring the evolutionary trees for them.
There are many tree reconstruction software programs available, and there are also online web sites that allow scientists to compare their results with other databases.
SuperTree is one of them.

SuperTree v2.0 works like a dream and reconstructs a much better tree than any of the other programs.
It runs on most versions of Windows, and relies on the PHYLIP 2.5 library.
SuperTree is a program that allows users to compare up to 12 trees and to reconstruct the most likely one, based on distance calculations.

Phylogeny, DNA content, and chromosome evolution: evidence from natural populations of Bolaea.
Joel F. Bloomgren, Kamalika Challa (2007).
Abstract.
Bolaea is a small genus of flowering plants with no current consensus regarding its circumscription and relationships. The genus is divided into two groups: northern and southern (K. Challa,
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This program gathers all the programs and tools necessary to run a variety of tree-searching algorithms for models derived from distance matrices and parsimony.
This package offers a large variety of statistics, consisting of tree scores such as tree length, number of clades, clade length, number of branches, etc.
Phylip runs on DOS and Windows from version 3.0 and up.

PHYLIP is a genome sequence analysis software package based on a hierarchical representation of evolutionary events.
While most commonly used for sequencing data, PHYLIP can also be used to reconstruct phylogenetic trees for datasets consisting of multiple sequence alignments.
Typical examples for this are the analysis of restriction sites, which often provide direct information about the evolutionary history of genomic sequences and gene-sequence data.

PHYLIP is a collection of programs and routines from the areas of bioinformatics, phylogenetics, molecular biology, mathematics, and statistics.
Most well known for its PATTINAT program for parsimony tree reconstruction, PHYLIP is often used for computer-based phylogenetic analysis.

PHYLIP is a genomics toolbox that includes a number of programs designed to facilitate phylogenetic analysis of nucleotide sequences and DNA data.
The package includes programs for parsing data in a specific sequence format, modeling evolutionary events in DNA, reconstructing phylogenetic trees from sequence information, and searching large data sets for phylogenetically relevant patterns.

PHYLIP is a collection of programs designed to facilitate phylogenetic analysis of nucleotide sequences and DNA data.
The package includes programs for parsing data in a specific sequence format, modeling evolutionary events in DNA, reconstructing phylogenetic trees from sequence information, and searching large data sets for phylogenetically relevant patterns.

PHYLIP is a genomics

What’s New In PHYLIP?

The PHYLIP project was initially conducted by the Statistical Genetics Department of the University of Michigan and the Department of Molecular Genetics and Microbiology at the University of Washington. The software, available for several versions, is now maintained by a group of users from a variety of institutions. The group includes the University of Connecticut, the University of Minnesota, the Carnegie Institution of Washington and the University of California at Santa Cruz, among others.
A complete documentation is available on the tool’s website.
Bibliography:
1. Statistical Methods for Genetic Research (Marshall and Blackburn, 1988, 1989).
2. Bioinformatics handbook – PHYLIP (Eds. J. Rosenberg and M. Hewlett, 1990, Chapman & Hall).
3. phylip.html
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System Requirements:

Mac OS X 10.7 or higher,
Intel Core 2 Duo (2.4 GHz) or equivalent,
4 GB of RAM,
1 GB of VRAM
Windows XP or higher,
Intel Pentium (2.0 GHz) or equivalent,
1 GB of RAM,
Optional Requirements:
USB Keyboard, USB Mouse, 1366×768 Display with support for 16:10 resolution, one USB 2.0 port
Install Notes:
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