Bioinformatics Phylogenetic analysis Phylogenetic Tree Construction

PHYLIP

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PHYLIP stands for PHYLogeny Inference Package. PHYLIP can develop trees from all three methods – distance, parsimony and likelihood. PHYLIP is a true “package”, which provides scores of programs and an extensive array of options. Besides sequences, PHYLIP can analyze frequency data, molecular sequences, fragments distance matrices, discrete characters and restriction site data. It Provides a diverse variety of methods for sequence and other data

 PHYLIP source code is written in the programming language C for a command line interface. It can be run easily on the LINUX/UNIX system, Mac OS and on Windows. No such technical expertise required for it and it is available as free of cost. PHYLIP does not perform the basic statistical analyses available in MEGA.

PHYLIP is probably the oldest widely-distributed phylogeny package. It is the sixth most frequently cited phylogeny package developed by Joe Felsenstein, Department of Genome Science at the University of Washington, after MrBayes, PAUP, RAxML, Phyml, and It has been in distribution since October, 1980, and has over 30,000 registered users. It is still being updated.

Advantages of PHYLIP

  • Free of cost
  • Good documentation 
  • Well known/widely used 
  • Possible to automate 
  • File formats supported by other packages
  • Calculate consensus tree from bootstraps 
  • flip nodes, re-root, re-arrange –run interactively
  • draw “tree-like” tree
  • draw unrooted tree

The programs in PHYLIP are controlled through a menu, which asks the users which options they want to set, and allows them to start the computation. Every line in the menu starts with a capital letter or number. It uses infile, intree, weights, categories and font file as input. The data are read into the program from a text file, which the user can prepare using any word processor or text editor. The PHYLIP programs re-use the same file names. Data files in the PHYLIP format. Most of the programs look for the data in a file called “infile” if they do not find this file they then ask the user to type in the file name of the data file. PHYLIP format is a plain text format containing exactly two sections: a header describing the dimensions of the alignment, followed by the multiple sequence alignment itself.

 The output is in the form of outfile, outtree, and plotfile. It is easy to analyze the wrong data (old “infile”) and overwrite (or mis-name) the output file. Trees written onto “outtree” are in the Newick format, an informal standard agreed to in 1986 by authors of a number of major phylogeny packages. Output results show only the number of taxa and length of alignment. The branches show the consensus frequencies, not the evolutionary branch lengths but the functions can be used to calculate branches for a single tree without any making a search.

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