hyphy1

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).