40 lines
1.8 KiB
Plaintext
40 lines
1.8 KiB
Plaintext
PHYLIP - Phylogeny Inference Package (version 3.6)
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PHYLIP (the PHYLogeny Inference Package) is a package of programs for
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inferring phylogenies (evolutionary trees). Methods that are
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available in the package include parsimony, distance matrix, and
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likelihood methods, including bootstrapping and consensus trees. Data
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types that can be handled include molecular sequences, gene
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frequencies, restriction sites, distance matrices, and 0/1 discrete
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characters.
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The programs are controlled through a menu, which asks the users which
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options they want to set, and allows them to start the
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computation. The data are read into the program from a text file,
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which the user can prepare using any word processor or text editor
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(but it is important that this text file not be in the special format
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of that word processor -- it should instead be in "flat ASCII" or
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"Text Only" format). Some sequence analysis programs such as alignment
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programs can write data files in the PHYLIP format. Most of the
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programs look for the data in a file called "infile" -- if they do not
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find this file they then ask the user to type in the file name of the
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data file.
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Output is written onto special files with names like "outfile" and
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"treefile". Trees written onto "treefile" are in the Newick format, an
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informal standard agreed to in 1986 by authors of a number of major
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phylogeny packages.
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PHYLIP is the most widely-distributed phylogeny package, and competes
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with PAUP to be the one responsible for the largest number of
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published trees. PHYLIP has been in distribution since 1980, and has
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over 6,000 registered users.
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Joe Felsenstein
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joe@genetics.washington.edu
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Department of Genetics
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University of Washington
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Box 357360
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Seattle, Washington 98195-7360, U.S.A.
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WWW: http://evolution.genetics.washington.edu/phylip.html |