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PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.
The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them from the original programs and avoid namespace conflict.
This is the EMBOSS integrated version of PHYLIP 3.69 If you require the original PHYLIP 3.69 distribution, you should obtain it from the author, Joe Felsenstein, at http://evolution.gs.washington.edu/phylip/software.html This file records the steps involved in making PHYLIP 3.69 compatible with EMBOSS as an EMBASSY package. The procedure is relatively simple, compared to other packages, as PHYLI more»
FCLIQUE(1e) EMBOSS Manual for Debian FCLIQUE(1e) NAME fclique - Largest clique program SYNOPSIS fclique -infile discretestates [-ancfile properties] [-factorfile properties] [-weights properties] [-cliqmin integer] [-outgrno integer] -outfile outfile [-trout toggle] -outtreefile outfile [-printdata bo more»
FCONSENSE(1e) EMBOSS Manual for Debian FCONSENSE(1e) NAME fconsense - Majority-rule and strict consensus tree SYNOPSIS fconsense -intreefile tree [-method list] -mlfrac float [-root toggle] [-outgrno integer] -outfile outfile [-trout toggle] -outtreefile outfile [-progress boolean] [-treeprint boolean] more»
FCONTML(1e) EMBOSS Manual for Debian FCONTML(1e) NAME fcontml - Gene f more»
FCONTRAST(1e) EMBOSS Manual for Debian FCONTRAST(1e) NAME fcontrast - Cont more»
FDISCBOOT(1e) EMBOSS Manual for Debian FDISCBOOT(1e) NAME fdiscboot - Boot more»
FDNACOMP(1e) EMBOSS Manual for Debian FDNACOMP(1e) NAME fdnacomp - DNA c more»
FDNADIST(1e) EMBOSS Manual for Debian FDNADIST(1e) NAME fdnadist - Nucle more»