--- name: "hyphy" section: "1" platform: "linux" package: "hyphy-pt" version: "2.5.69+dfsg-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/hyphy" --- # hyphy(1) Hypothesis testing using Phylogenies (pthreads version) ## NAME hyphy - Hypothesis testing using Phylogenies (pthreads version) ## DESCRIPTION usage: hyphy or HYPHYMPI \[-h\] \[--help\]\[-c\] \[-d\] \[-i\] \[-p\] \[BASEPATH=directory path\] \[CPU=integer\] \[LIBPATH=library path\] \[USEPATH=library path\] \[\ or \\] \[--keyword value ...\] \[positional arguments ...\] Execute a HyPhy analysis, either interactively, or in batch mode optional flags: - **-h** **--help** show this help message and exit - **-c** calculator mode; causes HyPhy to drop into an expression evaluation until 'exit' is typed - **-d** debug mode; causes HyPhy to drop into an expression evaluation mode upon script error - **-i** interactive mode; causes HyPhy to always prompt the user for analysis options, even when defaults are available - **-p** postprocessor mode; drops HyPhy into an interactive mode where general post-processing scripts can be selected upon analysis completion - **-m** write diagnostic messages to messages.log ### optional global arguments: - BASEPATH=directory path defines the base directory for all path operations (default is pwd) - CPU=integer if compiled with OpenMP multithreading support, requests this many threads; HyPhy could use fewer than this but never more; default is the number of CPU cores (as computed by OpenMP) on the system - LIBPATH=directory path defines the directory where HyPhy library files are located (default installed location is */usr/local/lib/hyphy* or as configured during CMake installation - USEPATH=directory path specifies the optional working and relative path directory (default is BASEPATH) - ENV=expression set HBL environment variables via explicit statements for example ENV='DEBUG\_MESSAGES=1;WRITE\_LOGS=1' - batch file to run if specified, execute this file, otherwise drop into an interactive mode - analysis arguments if batch file is present, all remaining positional arguments are interpreted as inputs to analysis prompts optional keyword arguments (can appear anywhere); will be consumed by the requested analysis - **--keyword** value will be passed to the analysis (which uses KeywordArgument directives) multiple values for the same keywords are treated as an array of values for multiple selectors usage examples: ### Select a standard analysis from the list : - hyphy **-i** Run a standard analysis with default options and one required user argument; - hyphy busted **--alignment** path/to/file Run a standard analysis with additional keyword arguments - hyphy busted **--alignment** path/to/file **--srv** No See which arguments are understood by a standard analysis - hyphy busted **--help** Run a custom analysis and pass it some arguments - hyphy path/to/hyphy.script argument1 'argument 2' Available standard keyword analyses (located in /home/nilesh/packages/hyphy/hyphy/res/) - meme \[MEME\] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution). - mh Merge two datafiles by combining sites (horizontal merge). - mv Merge two datafiles by combining sequences (vertical merge). - mcc Compare mean within-clade branch length or pairwise divergence between two or more non-nested cladesd in a tree - mclk Test for the presence of a global molecular clock on the tree using its root (the resulting clock tree is unrooted, but one of the root branches can be divided in such a way as to enforce the clock). - mgvsgy Compare the fits of MG94 and GY94 models (crossed with an arbitrary nucleotide bias) on codon data. - mt Select an evolutionary model for nucleotide data, using the methods of 'ModelTest' - a program by David Posada and Keith Crandall. - fel \[FEL\] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood). - fubar \[FUBAR\] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection). - fade \[FADE\] Test a protein alignment for directional selection towards specific amino acids along a specified set of test branches using FADE (a FUBAR Approach to Directional Evolution). - faa Fit a multiple fitness class model to amino acid data. - fmm "Fit a model that permits double (and triple) instantaneous nucleotide substitutions" - fst Compute various measures of F\_ST and (optionally) perform permutation tests. - slac \[SLAC\] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting). - sm Peform a classic and structured Slatkin-Maddison test for the number migrations. - sns Parse a codon alignment for ambiguous codons and output a complete list/resolutions/syn and ns counts by sequence/position - sw Perform a sliding window analysis of sequence data. - sa Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of sequential addition. - sbl Search an alignment for a single breakpoint. - spl Plot genetic distances (similarity) of one sequence against all others in an alignment, using a sliding window. Optionally, determine NJ-based clustering and bootstrap support in every window. This is a HyPhy adaptation of the excellent (but Windows only tool) SimPlot (and/or VarPlot) written by Stuart Ray (http://sray.med.som.jhmi.edu/SCRoftware/simplot/) - busted \[BUSTED\] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification). - bgm \[BGM\] Apply Bayesian Graphical Model inference to substitution histories at individual sites. - bva Run a selection analysis using a general discrete bivariate (dN AND dS) distribution; the appropriate number of rate classes is determined automatically. - brp Interpret bivariate codon rate analysis results. - bsel Split a tree into two clades (compartments) and a separating branch and test for equality of dN/dS between compartments and for selection along the separating branch using a series of Likelihood Ratio Tests. - bst Use the improved branch-site REL method of Yang and Nielsen (2005) to look for episodic selection in sequences. - bt Test whether a branch (or branches) in the tree evolves under different dN and dS than the rest of the tree. - absrel \[aBSREL\] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood). - acd Analyse codon data with a variery of standard models using given tree. - ad Analyse nucleotide or aminoacid data with a variery of standard models using given tree. - adn Analyse di-nucleotide data with a variery of standard models using given tree. - afd Analyse nucleotide data with a variery of standard models using given tree, estimating equilibrium frequencies as parameters - ana Run a selection analysis. - ai Peter Simmonds' Association Index (AI). - relax \[RELAX\] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation). - red Replace sufficiently close sequence with their MRCA - rpc Interpret analysis results. - rmv Remove sequences with stop codons from the data. - rble Use a series of random effects branch-site models to perform robust model-averaged branch length estimation under a codon model with episodic selection. - rclk Test for the presence of a global molecular clock on the tree. The tree is rooted at every possible branch. - rr Use relative rate test on three species and a variety of standard models - rrt Use relative ratio test on 2 datasets and a variety of standard models - prime \[PRIME\] - protein Compare the fit of several amino-acid substitution models to an alignment using AIC and c-AIC. - prr Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file. - prrti Given a list of files (and optionally genetic code tables), perform relative ratio tests on all possible pair of the data files. - pdf Read sequence data, select a contiguous subset of sites and save it to another datafile. - phb Run an example file from our book chapter in 'The Phylogentic Handbook' (2nd edition). - psm Test for positive selection using the approach of Nielsen and Yang, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS\>1. Multiple subsets of one data set with shared dN/dS. - parris A PARtitioning approach for Robust Inference of Selection (written by K. Scheffler) - contrast-fel \[Contrast-FEL\] "Perform a site-level test for differences in selective pressures between predetermined sets of branches." - conv Translate an in-frame codon alignment to proteins. - corr Assess the correlation between phylogenetic and compartment segregation using generalized correlation coefficients and permutation tests. - cod Compare all 203 reversible nucleotide models composed with MG94 to extend them to codon data, and perform LRT and AIC model selection. - cmp Use a series of LR tests to decide if dN and dS rate distributions are the same or different between two codon alignments. - caln Align coding sequences to reference (assuming star topology) using a codon-based dynamic programming algorithm (good for fixing multiple frameshifts). Designed with within-patient HIV sequences in mind. - clg Remove 'gappy' sites from alignments based on a user-specified gap threshold. - cln Convert sequence names to HyPhy valid identifiers if needed and replace stop codons with gaps in codon data if any are present. - clsr Partition sequences into clusters based on a distance matrix. - clst Apply clustering methods for phylogeny reconstruction (UPGMA,WPGMA,complete or minimal linkage) to nucleotide, protein and codon data, using MLE of pairwise distances with user-selectable models. These methods produce trees with global molecular clock. - leisr Infer relative evolutionary rates on a nucleotide or protein alignment, in a spirit similar to Rate4Site (PMID: 12169533). - lz Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences - lclk Test for the presence of a local molecular clock. Every subtree of the given tree is subjected to the clock constraint, while the remainder of the tree is free of the clock constraint. - lht A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. \[Contributed by Olivier Fedrigo\]. - tc Test whether a group of sequences in a sample cluster together - ts Perform an exhaustive tree space search for nucleotide or protein data with user-selectable models. Should only be used for data sets with less than 10 taxa! - dtr Read sequence data (#,PHYLIP,NEXUS) and convert to a different format - dist Generate a pairwise sequence distance matrix in PHYLIP format. - kh Perform a Kishino-Hasegawa test on two competing phylogenies - ub Obtain an upper bound on the likelihood score of a dataset. - nuc Compare all 203 reversible nucleotide models and perform LRT and AIC model selection. - nj Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of neighbor joining. - ny Test for positive selection using the approach of Nielsen and Yabg, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS\>1. - gard \[GARD\] Screen an alignment using GARD (requires an MPI environment). ## AUTHOR This manpage was written by Nilesh Patra for the Debian distribution and\ can be used for any other usage of the program.