HYPHY(1) User Commands HYPHY(1)

hyphy - Hypothesis testing using Phylogenies (pthreads version)

usage: hyphy or HYPHYMPI [-h] [--help][-c] [-d] [-i] [-p] [BASEPATH=directory path] [CPU=integer] [LIBPATH=library path] [USEPATH=library path] [<standard analysis name> or <path to hyphy batch file>] [--keyword value ...] [positional arguments ...]

Execute a HyPhy analysis, either interactively, or in batch mode optional flags:

show this help message and exit
calculator mode; causes HyPhy to drop into an expression evaluation until 'exit' is typed
debug mode; causes HyPhy to drop into an expression evaluation mode upon script error
interactive mode; causes HyPhy to always prompt the user for analysis options, even when defaults are available
postprocessor mode; drops HyPhy into an interactive mode where general post-processing scripts can be selected upon analysis completion
write diagnostic messages to messages.log

defines the base directory for all path operations (default is pwd)
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
defines the directory where HyPhy library files are located (default installed location is /usr/local/lib/hyphy or as configured during CMake installation
specifies the optional working and relative path directory (default is BASEPATH)
set HBL environment variables via explicit statements for example ENV='DEBUG_MESSAGES=1;WRITE_LOGS=1'
if specified, execute this file, otherwise drop into an interactive mode
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

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:

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] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution).
Merge two datafiles by combining sites (horizontal merge).
Merge two datafiles by combining sequences (vertical merge).
Compare mean within-clade branch length or pairwise divergence between two or more non-nested cladesd in a tree
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).
Compare the fits of MG94 and GY94 models (crossed with an arbitrary nucleotide bias) on codon data.
Select an evolutionary model for nucleotide data, using the methods of 'ModelTest' - a program by David Posada and Keith Crandall.
[FEL] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood).
[FUBAR] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection).
[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).
Fit a multiple fitness class model to amino acid data.
"Fit a model that permits double (and triple) instantaneous nucleotide substitutions"
Compute various measures of F_ST and (optionally) perform permutation tests.
[SLAC] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting).
Peform a classic and structured Slatkin-Maddison test for the number migrations.
Parse a codon alignment for ambiguous codons and output a complete list/resolutions/syn and ns counts by sequence/position
Perform a sliding window analysis of sequence data.
Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of sequential addition.
Search an alignment for a single breakpoint.
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] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification).
[BGM] Apply Bayesian Graphical Model inference to substitution histories at individual sites.
Run a selection analysis using a general discrete bivariate (dN AND dS) distribution; the appropriate number of rate classes is determined automatically.
Interpret bivariate codon rate analysis results.
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.
Use the improved branch-site REL method of Yang and Nielsen (2005) to look for episodic selection in sequences.
Test whether a branch (or branches) in the tree evolves under different dN and dS than the rest of the tree.
[aBSREL] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood).
Analyse codon data with a variery of standard models using given tree.
Analyse nucleotide or aminoacid data with a variery of standard models using given tree.
Analyse di-nucleotide data with a variery of standard models using given tree.
Analyse nucleotide data with a variery of standard models using given tree, estimating equilibrium frequencies as parameters
Run a selection analysis.
Peter Simmonds' Association Index (AI).
[RELAX] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation).
Replace sufficiently close sequence with their MRCA
Interpret analysis results.
Remove sequences with stop codons from the data.
Use a series of random effects branch-site models to perform robust model-averaged branch length estimation under a codon model with episodic selection.
Test for the presence of a global molecular clock on the tree. The tree is rooted at every possible branch.
Use relative rate test on three species and a variety of standard models
Use relative ratio test on 2 datasets and a variety of standard models
[PRIME]
Compare the fit of several amino-acid substitution models to an alignment using AIC and c-AIC.
Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file.
Given a list of files (and optionally genetic code tables), perform relative ratio tests on all possible pair of the data files.
Read sequence data, select a contiguous subset of sites and save it to another datafile.
Run an example file from our book chapter in 'The Phylogentic Handbook' (2nd edition).
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.
A PARtitioning approach for Robust Inference of Selection (written by K. Scheffler)
[Contrast-FEL] "Perform a site-level test for differences in selective pressures between predetermined sets of branches."
Translate an in-frame codon alignment to proteins.
Assess the correlation between phylogenetic and compartment segregation using generalized correlation coefficients and permutation tests.
Compare all 203 reversible nucleotide models composed with MG94 to extend them to codon data, and perform LRT and AIC model selection.
Use a series of LR tests to decide if dN and dS rate distributions are the same or different between two codon alignments.
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.
Remove 'gappy' sites from alignments based on a user-specified gap threshold.
Convert sequence names to HyPhy valid identifiers if needed and replace stop codons with gaps in codon data if any are present.
Partition sequences into clusters based on a distance matrix.
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.
Infer relative evolutionary rates on a nucleotide or protein alignment, in a spirit similar to Rate4Site (PMID: 12169533).
Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences
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.
A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo].
Test whether a group of sequences in a sample cluster together
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!
Read sequence data (#,PHYLIP,NEXUS) and convert to a different format
Generate a pairwise sequence distance matrix in PHYLIP format.
Perform a Kishino-Hasegawa test on two competing phylogenies
Obtain an upper bound on the likelihood score of a dataset.
Compare all 203 reversible nucleotide models and perform LRT and AIC model selection.
Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of neighbor joining.
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] Screen an alignment using GARD (requires an MPI environment).


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.

January 2021 hyphy 2.5.26