====== PHYLIP ====== {{phylip_logo.gif?150}} \\ **[[http://evolution.genetics.washington.edu/phylip/doc/main.html|PHYLIP]]** \\ Version 3.69 (September 2009)\\ PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). 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. ===== Program information ===== * written in C * Windows * Mac OS X * Mac OS 9 * UNIX * Linux ===== Data type handled ===== * nucleotide sequences * protein sequences * gene frequencies * restriction sites * restriction fragments * distances * discrete characters * continuous characters ===== Input Files ===== ==== nucleotide sequences ==== For most of the PHYLIP programs, information comes from a series of input files, and ends up in a series of output files: ------------------- | | infile ---------> | | | | intree ---------> | | -----------> outfile | | weights --------> | program | -----------> outtree | | categories -----> | | -----------> plotfile | | fontfile -------> | | | | ------------------- Input data such as DNA sequences comes from a file whose default name is infile. If the user supplies a tree, this is in a file whose default name is intree. Values of weights for the characters are in weights, and the tree plotting program need some digitized fonts which are supplied in fontfile (all these are default names). \\ * first line: the number of species and the number of characters. These are in free format, separated by blanks * next lines: information for each species, starting with a ten-character species name (which can include blanks and some punctuation marks. The name should be ten characters in length, filled out to the full ten characters by blanks if shorter), and continuing with the characters for that species. The name should be on the same line as the first character of the data for that species. * In the discrete-character programs, DNA sequence programs and protein sequence programs the characters are each a single letter or digit, sometimes separated by blanks. In the continuous-characters programs they are real numbers with decimal points, separated by blanks: Latimeria 2.03 3.457 100.2 0.0 -3.7 * The conventions about continuing the data beyond one line per species are different between the molecular sequence programs and the others. The molecular sequence programs can take the data in "aligned" or **"interleaved" format**, in which we first have some lines giving the first part of each of the sequences, then some lines giving the next part of each, and so on. Thus the sequences might look like this: 6 39 Archaeopt CGATGCTTAC CGCCGATGCT HesperorniCGTTACTCGT TGTCGTTACT BaluchitheTAATGTTAAT TGTTAATGTT B. virginiTAATGTTCGT TGTTAATGTT BrontosaurCAAAACCCAT CATCAAAACC B.subtilisGGCAGCCAAT CACGGCAGCC TACCGCCGAT GCTTACCGC CGTTGTCGTT ACTCGTTGT AATTGTTAAT GTTAATTGT CGTTGTTAAT GTTCGTTGT CATCATCAAA ACCCATCAT AATCACGGCA GCCAATCAC * extension: .txt * blanks within sequences are allowed to make them easier to read, also digits are ignored in the sequence * It is important that the number of sites in each group be the same for all species * In the **sequential format**, the character data can run on to a new line at any time. Thus it is legal to have: Archaeopt 001100 1101 or even: Archaeopt 0011001101 \\ === example: === * the simplest version of the input data file looks something like this: 6 13 Archaeopt CGATGCTTAC CGC HesperorniCGTTACTCGT TGT BaluchitheTAATGTTAAT TGT B. virginiTAATGTTCGT TGT BrontosaurCAAAACCCAT CAT B.subtilisGGCAGCCAAT CAC * example of interleaved format: 5 42 Turkey AAGCTNGGGC ATTTCAGGGT Salmo gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT Chimp AAACCCTTGC CGTTACGCTT Gorilla AAACCCTTGC CGGTACGCTT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA AAACCGAGGC CGGGACACTC AT AAACCATTGC CGGTACGCTT AA * sequential format the same sequences would be: 5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA ==== Distance Matrix ==== * first line of the input file contains the number of species * There follows species data, starting with a species name. * species name is ten characters long, and must be padded out with blanks if shorter * For each species there then follows a set of distances to all the other species (allow the distance matrix to be upper or lower triangular or square). The distances can continue to a new line after any of them. If the matrix is lower-triangular, the diagonal entries (the distances from a species to itself) will not be read by the programs. If they are included anyway, they will be ignored by the programs, except for the case where one of them starts a new line, in which case the program will mistake it for a species name and get very confused. === examples: === * sample input matrix, with a square matrix: 5 Alpha 0.000 1.000 2.000 3.000 3.000 Beta 1.000 0.000 2.000 3.000 3.000 Gamma 2.000 2.000 0.000 3.000 3.000 Delta 3.000 3.000 0.000 0.000 1.000 Epsilon 3.000 3.000 3.000 1.000 0.000 * sample lower-triangular input matrix with distances continuing to new lines as needed: 14 Mouse Bovine 1.7043 Lemur 2.0235 1.1901 Tarsier 2.1378 1.3287 1.2905 Squir Monk 1.5232 1.2423 1.3199 1.7878 Jpn Macaq 1.8261 1.2508 1.3887 1.3137 1.0642 Rhesus Mac 1.9182 1.2536 1.4658 1.3788 1.1124 0.1022 Crab-E.Mac 2.0039 1.3066 1.4826 1.3826 0.9832 0.2061 0.2681 BarbMacaq 1.9431 1.2827 1.4502 1.4543 1.0629 0.3895 0.3930 0.3665 Gibbon 1.9663 1.3296 1.8708 1.6683 0.9228 0.8035 0.7109 0.8132 0.7858 Orang 2.0593 1.2005 1.5356 1.6606 1.0681 0.7239 0.7290 0.7894 0.7140 0.7095 Gorilla 1.6664 1.3460 1.4577 1.5935 0.9127 0.7278 0.7412 0.8763 0.7966 0.5959 0.4604 Chimp 1.7320 1.3757 1.7803 1.7119 1.0635 0.7899 0.8742 0.8868 0.8288 0.6213 0.5065 0.3502 Human 1.7101 1.3956 1.6661 1.7599 1.0557 0.6933 0.7118 0.7589 0.8542 0.5612 0.4700 0.3097 0.2712 ===== How to cite ===== Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. \\ Or if the editor for whom you are writing insists that the citation must be to a printed publication, you could cite a notice for version 3.2 published in Cladistics:\\ Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.